CopyPod & File Formats

[finminer]

60GB 5G - I lost my HD thus my whole library, but everything was on the iPod. Many many songs were M4A format from my 400+ CD collection. So after replacing the HD, I got Copypod and wrote the iPod back and started rebuilding my library. However, all those files that were from CD, the M4A files, were written back as MP3's and show up that way in iTunes. Did I do something wrong? I'd prefer to have them in M4A as the sound quality is better, right? I haven't synched the iPod, do I need to back it up again with a different setting?

Thanks in advance!
Allan