Itunes not syncing all music from library

I've recently transferred from a previous account - it was shared - to my own. It was on a seperate computer and some of the songs from the previous library (I stopped transferring them after a point) had been stored into the library on the computer I'm using now.

When I go to sync I notice it says that certain files can't be found and it doesn't sync everything completely. Now, this would make sense if the music I had didn't come from CDs. I even deleted one CD, imported it in full, synced it, had the full album show up, then went to sync it again only to have the majority of the album disappear. I've tried to sync it four or five times and it's all the same songs that allegedly "aren't there."

Does anyone know what's going on, or even how to fix this?

If it helps I have an iPod touch 4.