BuddyPress.org

There’s only been a beta 1, beta 2 and RC1 release (and trunk of course). If you started making your changes on RC1 then at least that’s a slight clue. Since by your own admission you’ve heavily hacked the code around, it is very hard to understand why this might be happening. I think it must be due to one or more of the changes you have made as I’ve never seen this problem before either.

Do you get anything in your web server’s error log when this happens? e.g. when you are on Members and try to go back to Home.