Maybe could you also create a new test score for solo bassoon and use the articulations/expressions which seem to work improperly. If everything goes right in such a score then it's certainly not the VSL bassoon which leads you into troubles.
Sometimes I have timing problems with Sibelius 6 when I play big scores. Have you tried to play your score after deactivating live playback, live tempo (blue lightning and conductor icons on the transport bar) and any rubato/expressivo style (Play --> Performance --> expressivo/rubato = "meccanico") ? That may solve timing problems on my side.
Wouldn't you have written accidentally hidden informations like a metric modulation for your bassoon part ?
Good luck anyway...
Michaël