To cut and paste from another post I just made:
Yeah, well, unfortunately, Apple/iTunes/iPod app code music a little differently (some would say it is annoying odd).
It's best to not to try to put music onto the iPad for playing specifically through the iPod app. It's best to leave that kind of synching to iTunes.
That doesn't stop you from SSHing in and putting music on the iPad (I think there are music playing apps you can use, but I don't remember any off the top of my head). Just don't try to put it in the iPod section. Won't work (AFAIK).
Marilyn