BuddyPress.org

This the same operating system version? Same host? Upgrade apache?

It worked for 2.6.5. Well, it doesn’t work that way now. For some unknown reason.

You have apache AND wpmu handling home.php and index.php in some fashion that doesn’t work any more. Both of them have sequences and overrides and whatever. You have multiple index files and multiple applications having possible control over them in some fashion that can’t be debugged.

Abandon what doesn’t work and figure out a different way of doing it.