Re: Plugins not showing up in WPMU
Did you install them in /mu-plugins/ or just /plugins/?
Plugins installed in /mu-plugins/, such as BuddyPress, will not show up on the plugins page as plugins in this folder are automatically activated across the entire WPMU install.
On the other hand, if plugins are only needed on a blog-by-blog basis they are to be installed in the regular /plugins/ directory and will be shown on the plugins page just as in regular wordpress.
The BuddyPress plugins are supposed to be installed in /mu-plugins/ per step 3 of the instructions.