Converting Song2Sequence

Just finished doing 3 sequences using Full Lever... no over dubs. At the song mode I did the song organization, and as converting the song(Finish Production) into a sequence I play it and the outcome is not what I wanted, it plays different instruments on some parts, it doesn't seem to follow through on what I press maybe?!...
Anyone has have this before? or I just did something wrong....

Oh and on the over dub I don't think it'll effect anything right... & of course all my wav. samples have nothing wrong w/ it.

LMK whaaa'zurr.

tried remaking my sequences today, and did my song setup... the outcome was the same as before... there must be something wrong that I'm doing or it might be the samples I use.