Re: permalinks problem
The first steps are to distill your install down to the lowest common denominator. That means disabling all plugins except BuddyPress and switching to the default theme framework that comes with BP. If the problem goes away, then it has something to do with your theme and/or plugins.
If that is the case, they the next step is to reactivating each plugin one at a time until the issue returns. If it does not return, then switch to your custom theme. If it returns, then there is an issue with your custom theme.