Hi all – Just wanted to chime in and echo what Ray’s said. Basically, BP itself is in the process of transitioning from an old version of bbPress (v1.x – this is the “bundled forums” that Ray mentions above) to the new version (v2.x). The upcoming major BuddyPress release, BP 1.7, is actually formally retiring the old-school forums – they’ll still work, but they won’t be offered as an option when installing BP from scratch.
So, basically, Ray’s right that using bbPress 2.x is the best way forward. In my experience, the migration tool that Ray alludes to is pretty robust, so as long as you have taken database backups, I would feel comfortable running it. If things go awry during the migration process, feel free to reach out and I’ll see what I can do to help.