BuddyPress.org

I was wondering if this is still the case for 1.2 as I keep stumbling across functionality that doesn’t jive on a sub-dir style install

If you mean you have found bugs, please report them on https://trac.buddypress.org/.

Early versions of BP didn’t work 100% properly on subdirectory installs but as far as I know it shouldn’t make a difference nowadays (from BuddyPress’ perspective).