I'm assuming that the best place to ask this would be the bbPress forums and I've done that, but on the off chance someone else with WPMU has experienced this I thought I'd also note the problem here.
I successfully integrated bbPress into a WPMU site, but I have the oddest issue. If I log in through WPMU, bbPress works fine save that I can't access the bbPress admin panel. It just redirects me back to the forums. However it doesn't do this if I log in via the forums -- and regardless I can always access the WPMU admin panel.
Very odd.