It's not very clear to me in the OP if the problem is audio or MIDI here, but if it's MIDI related: some runaway MIDI controller left behind? I found a program change occasionally i couldn't remove with BIAB's pianoroll editor. Usually the fix is to erase/reset the track completely, or even to import the MIDI file in a proper DAW where you can manhandle the data.

Funny one for the Halion Sonic users: if you leave Local ON active in Midi options, you'll get some low level 'bang a gong' sound like a bed spring when file playback starts with BIAB.

BTW a list of controllers on Bob Norton's site with some useful advice: http://www.nortonmusic.com/midi_cc.html