Rich,
I'm not quite sure what to make of your problem. It's not one that I'm familiar with.
Please correct me if I'm wrong but the way I'm interpretting your post is...
1. You are referring to the 2-bar count-in that's built into BIAB.
2. The problem sounds are on the bass track.
3. I'm assuming that you know that the problem lies with the bass track because you've sequentially solo'd each track to isolate which one it is. Is this a correct assumption?
If the above applies...
When you go into Editable Notation Mode, to see the notation on the bass track, you need to select the button I've highlighted on the image below. Did you do this?
Also,
Are you using Realtracks or MIDI tracks?
If you could do a Printscreen of your main screen and then post the image, it would be very beneficial for all of us to see. (The link below will take you to a thread that explains how to post images if you are unsure how to do this.)
http://www.pgmusic.com/forums/ubbthreads.php?ubb=showflat&Number=386690#Post386690Regards,
Noel