Ok, everybody, this is my attempt at summarizing all the information we've managed to pull together from the old, enormous thread into one post. I will continue to update this post as more information is gathered so that there will be a single post with the most current information.
ISSUE
When connecting your iPod to your computer, a yellow bubble pops up in iTunes telling you that your "Play Counts" or "SysInfo" files are corrupted, and asks that you run "chkdsk."
CONTACT WITH APPLE
As many of you know, I have been in contact with one of the supervisors at Apple Customer Service. When we spoke last, he said that they investigated the issues surrounding these "corrupt files" and "it does not appear to be a very widespread problem." I'm not really sure how they've managed to determine that, considered the sheer number of people on this forum and at the Apple Discussion Forums (see the end of this post for more information on this) who are reporting this problem. You would have to assume that there are many other iPod owners who have experienced this problem but are not members of this forum, etc., who's voices have not been heard.
WHAT IS CAUSING THIS PROBLEM?
Apple has now recognized that this problem is caused by the 11-15-04 (and later) iPod Updater. However, the the problem manifests itself after the iPod goes into a deep sleep. There is hope that this problem will be resolved in the near future in a new iPod Updater.
SO, WHAT DO YOU DO TO FIX THIS PROBLEM?
The solution, unfortunately, is only temporary. To date, we have been able to determine four fixes.
[Fix #1]: Fix #1 is the easiest method, but is also the most unreliable and the most short lived solution. Simply doing a soft reset or a hard reset on the iPod will get rid of the error message. To do a soft reset, simply press and hold down the menu+select keys simultaneously until the Apple logo appears and the iPod reboots. To do a hard reset, follow the same steps but plug your AC adapter into your iPod first.
The next time you connect your iPod to your computer, the error message will not appear. However, as mentioned, this solution is short lived. For some unknown reason, the error message will return. It may return in a day, two days, three days, a week, whenever. There is no consensus as to when it will return and there are no patterns, but it will return. For example, the return of this error message following a reset is not limited to times when the iPod awakens from a "deep sleep." There are simply no patterns.
[Fix #2]: Fix #2 is more reliable and can be a long term solution. This fix involves running the "chkdsk" utility. Thanks go to BobZoron for posting step-by-step instructions on how to do this. Here's his solution:
Update to Fix #2
After completing fix #2 (above), the iPod will be fixed and you will no longer get the error message if you prevent the iPod from going into a deep sleep. Accordingly, it is necessary that you prevent your iPod from going unused for more than 36 hours.
A user at the Apple Discussion Forums (named JimUK69) has come up with a clever solution to making sure your iPod doesn't enter a deep sleep:
(1) Create a new playlist with either no songs or a very short song.
(2) Set a daily alarm which wakes the iPod up at 3am, and plays this empty or very short playlist.
By doing this, you will ensure your iPod is used for at least a few seconds every single day, and it will not go back into a deep sleep. Therefore, you can now wait patiently for Apple to get around to releasing an official fix.
This post will be dedicated to eliminating theories about the cause of this error message. It is important to keep a list of things that are not the cause of this problem so that we don't keep "spinning our wheels" on issues that have already been conclusively dismissed.
To date, either Apple representatives or other iPod users have speculated that the error message results from:
(a) A fragmented iPod hard drive,
(b) Disconnecting the iPod from your computer while the "do not disconnect" error message is still displayed,
(c) Fault USB 2.0 connection.
Evidence Against Claimed Possible Causes
(a) Fragmented iPod hard drive.
Several users on the iPodlounge and on the Apple Discussion Forums have used the latest iPod Updater to do a full restore of their iPods. Following a full restore, their iPods will no longer be fragmented. Yet, as soon as their iPods go into a deep sleep, the error message returns on what is now a completely defragmented hard drive. Therefore, fragmentation is definitely not the cause of this error message.
(b) Disconnecting the iPod while the "do not disconnect" warning is displayed.
Many users (myself included) have never disconnected their iPods while the "do not disconnect" warning is displayed. I think it is pretty clear that this has nothing to do with the error message.
(c) Fault USB 2.0 connection.
This one was pretty easy to knock off the list. People who exclusively use Firewire to connect to their computer are also experiencing this problem, so there is no connection to USB 2.0.
Warning To Users Of Newer 4g iPods.
Fix #3 and #4 come with a warning regarding newer 4g iPods. It appears that newer 4g iPods (defined as iPods manufactured in December, 2004 or later) are not capable of being rolled back to firmware version 3.0.1. Therefore, it will be fruitless for you to attempt either one of these fixes.
Therefore, as recommended above, if you are experiencing this problem and have a newer 4g iPod, follow BobZoron's instructions outlined in Fix #2 (above) and fix the problem with CHKDSK. Then, make sure your iPod does not go into a deep sleep until Apple releases an official fix for this problem.
Excellent information on this problem. Let's hope Apple comes up with a fix soon. I've ordered an ipod shuffle - currently using a 4G 20 ipod. I will be using the shuffle with the same PC. Since the last updater indicated that it added support for the shuffle, I'm assuming that if I roll back to the older updater to solve this problem, the Shuffle won't work. Does anyone have any ideas on this?
You correctly interpreted what I was asking. I tend to agree with the not sleeping thing, although once I get the shuffle (which I will use for my daily workout, I'll have to make more of an effort to keep the ipod from going into deep sleep.
Hi, a quick google search found the answer to my iPod problem here in this thread, talk about a frustrating problem!
Well I run fix #2 talked about here, and chkdsk found the corrupt file and fixed it, the error no longer pops up, however my iTunes software still crashes as soon as it opens when the iPod is connected.
I have uninstalled and reinstalled many times, no idea what else to try, hope someone here might have a better idea! I hope!
Sure hope to see Apple patch this up soon!! Just because some of us don't use our iPods daily we sure shouldn't have to put up with this!!!
Was glad to find this forum and thread!
Thanx in advance for any further help!
-Marie
Well said - plenty of time on your hands - Hmm?
Well, I was hoping not to delurk in a problem thread but circumstances seem to have dictated otherwise. In any case I just finished reading the 15 page consolidated thread about this problem and I'd like to thank all those that posted fixes on this problem. I used "solution 1" and did a reset, but if (or when) the problem comes back I'll run CHKDSK.
If it's helpful, I'll add the circumstances of my error. I had received my 4G in late December. I didn't get the CHKDSK error until tonight. I have been running the latest versions of iTunes since it was first released.
If I can think out loud for a moment and ask are people getting these errors after their iPod reaches a certain point in it's capacity? In my latest sync the iPod had 7.76 Gigs of music on it. Is it possible that the amount of data on the drive impacts it's ability to come out of a deep sleep without problems?
I figured I'd toss this out there until Apple comes up with something more definitive. Again, thanks for the info that has been posted and I look forward to posting more but hopefully not due to errors on my iPod... 
I was just experiencing this very frustrating problem and have tried very hard to get some answers and get it resolved. I put together this thread in an effort to help people until we finally get a fix from Apple.
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NOTE: This thread refers to a problem with 4th generation iPods running pre-"2005-06-26 iPod Updater" firmware. The problem related to a "corrupt" "play counts" and/or "SysInfo" file, resulting in a message in iTunes telling you to "run chkdsk."
If you have a 4th generation iPod *AND* you're running pre-"2005-06-26 iPod Updater" firmware *AND* you're seeing this error message, read below and follow these instructions.
If you have any other generation iPod or you're running a newer firmware, this thread does not relate to your particular problem. Please search other threads for more pertinent information. If you do not find any existing threads, please start a new thread explaining your specific problem.
Thank you.
This is the revised and updated thread concerning the "corrupt file" and "run chkdsk" issues.
Summary Of Problem
When connecting your iPod to your computer, a yellow bubble pops up in iTunes telling you that your "Play Counts" or "SysInfo" files are corrupted, and asks that you run "chkdsk."
Old Thread
Here is the old (very long) thread discussing this issue:
http://forums.ipodlounge.com/showthr...threadid=66101
Reason For Starting This New Thread
This new thread will provide a summary of all information known to date, and will be updated when new information comes in. The old thread is now filled with inaccurate and outdated information, so I felt it was time to start a new one and have a fresh start.
UPDATE: AUGUST 8, 2005 *****IMPORTANT UPDATE***** PLEASE READ
The information contained below refers to a problem with the March, 2005 Updater.
The newest Updater (the 2005-06-26 iPod Updater) has apparently resolved the "chkdsk" problem. It has been reported by many users that updating to this newest firmware has resolved this problem.
WARNING: Although the 2005-06-26 Updater has solved the "chkdsk" error problem, it has introduced a new problem. Namely, smart playlists no longer dynamically update on the iPod itself. To get your smart playlists to update on the iPod, you need to connect the iPod to iTunes. For more information about this new problem, please see this thread:
http://forums.ilounge.com/showthread...hreadid=104558
So, what do you do now?
Well, if you're experiencing the "chkdsk" error problem and DO NOT CARE about smart playlists, download the 2005-06-26 Updater and update the firmware on your iPod. The "chkdsk" error problem should now be resolved.
If you DO CARE about smart playlists and want the ability to have them update on the iPod itself, DO NOT update to the 2005-06-26 Updater. Instead, keep your current firmware and read below and select one of the alternate "fixes." Then, continue to use this fix until the NEXT iPod Updater gets released -- one that will hopefully fix both the "chkdsk" problem and the new smart playlist problem.