Messed around with this more, used an OS X script to rename all tracks within iTunes to remove any track numbers, which didn't work.
I then took 2 albums, 1 that was ok and 1 that was not and compared everything on them. I discovered their ID3 tags were different versions, so I used iTunes to set the versions the same, still no good.
It's very strange because some of the stuff I ripped myself from CDs is good, while others is not. So I can't even write it off as how the MP3s were created. I wonder is there something internal that can not even be changed or seen, related to the original cds.
