BIABman,
One way to do what you want would be to have two tracks of bass. For one track, generate the entire song in Part A style.Then change all the Part Markers to Part B style and generate the second bass track. You could then use Bar Settings to have two bars of the first track play (while the second track is muted) followed the two bars of the second track playing (while the first track is muted). This could also be accomplished with volume automation if you have a latter version of BIAB.
Thanks Noel. I got your first suggestion to work just now.

But there are still some problems.
On the second repeat, Bass 1 starts to walk (like it's playing a 1b part) !
How can I tell BIAB to do exactly the same for the second repeat (with the bass parts)?
Also, after the above is fixed, and the first two repeats are played, I need to run through the chorus 5 times (with repeats) with the walking bass playing throughout.
I hate copying 100's of bars, so I'd prefer to have a solution where I just see the first and second repeat on screen (like right now).