Ok, Thanks for your help.
Anyways, just if you wanted to try it yourself maybe I'm doing something wrong here are some tracks that just won't loop:
http://www.sendspace.com/file/i5u9sa
You don't have to try it if you don't want to. I can still loop them the other way.
EDIT: Nevermind. I think I know why now. You see if I do each track one by one, like WorkA, WorkB, WorkC, etc. and convert them to GBA and save them as seperate tracks they can loop because each track is like a different song. However, if I do it my method and just compile the whole song, each track has a different amount of measures and beats and each track is part of one song. So basically, the loop doesn't work because each track has to have the same amount of measures and same amount of beats in its last measure as all the other tracks in which it is part of the song in order for it to loop successfully (If each track is part of one song; meaning all the tracks were assembled together).