bugs in song mode

I use the track mutes allot in my sequences. When all my sequnces are created, i lay it out in song mode and conver it into 1 big sequnce. I noticed that some of the track mutes I recorded dont work. when i go back to song mode and hit play, the track mutes work fine. I have tried turning the track mute feature on and re-recording the mutes in the big sequnce i created, but it doesnt seem to record.
I think i have read somewhere that some samples arent being triggered when the sequences are created from others in here. Can anyone confirm these bugs?