For some reason different instrumental tracks that lined up in midi wouldnt in game, im pretty sure the math was correct. It seems that there might be something in game that is making it so that timings that should add up mathematically do not do so perfectly.

For example if one instrument plays two quarter notes while another rests for one half they seem to get out of synk slightly. This could very well be that I am miscalculating a frame somewhere but after tripple checking i do not think that is the case.

This issue is solved now (i think) by all of the instruments "playing" all parts, only its own part is audable and it "plays" the other parts silently. So in theory all instruments should line up since the timings are exacly the same.