BuddyPress.org

Before I updated my BP install last week, I noticed some similar odd search behavior. I, too, was running r1324 before I updated to the then latest trunk. After updating, the issue has gone away. I have not looked in trac to see if there was a specific bug that fixed this or if it was something else I did

However, if you have not yet read this article, you may find it interesting.

Google Custom Search for BuddyPress / WordPress MU