It can be a problem, but I can't remember exactly why. I did the same thing you did; I set up an iPod on my PC first, and then tried to use it on the Mac. Now, I think the Mac recognized the songs, but the iPod disk was in a PC format (FAT32?).
The problem may lie in creating two partnerships. As long as you have a backup of the music, give it a try though. You can always fall back on your backup.
Mike LaRiviere