I have iTunes 4.9 and the latest update for my 4G iPod. This morning I popped the iPod into the dock to sync any new podcasts that had downloaded. When I ejected the iPod all of my podcasts were gone from it. All my music was there, though.
I have iTunes set to sync all of my podcasts to my iPod, but only the podcasts I have checked. I re-synced and still no podcasts. So I went into the settings and set it to sync ALL podcasts, then went back and re-selected the setting to only sync checked podcasts and everything is back to normal now.