I'm traveling so I can't verify what build I have, but I seem to recall updating it within the last 3-4 months. I tried different plugins--Kontakt, Dimension Pro, Alchemy--plus an Acoustica instrument. I had the same problem with all of them.
Maybe I need to try muting midi tracks and see if that helps. I've noticed that importing BIAB-created midi tracks in Mixcraft is not as smooth as into Sonar (e.g., when I import a single track, Mixcraft shows blank clips for each of the tracks muted in BIAB, which is odd since as far as I can tell, BIAB only renders the single midi track).
But as I noted, this only seems to become a problem after I've added several midi tracks, either be playing them in or importing them from BIAB or Stylus RMX. I can't duplicate the problem by importing the usual 5-track mix from BIAB. And it doesn't seem to be a Stylus problem because it happens on songs with no Stylus tracks (plus there's an obvious melodic character to the unwanted notes).
Sounds like you've not encountered this before...