I can confirm this problem: Sitewide activity feed doesn’t work either (404 page not found) and pressing the delete button on activity stream items takes me to a 404 after a confirmation dialog, too. Failing target URL is http://[DOMAIN]/activity/delete/%5BID%5D?_wpnonce=%5BTOKEN%5D
I too am running wpmu 2.8.6 and bp 1.1.3 (subdirectories).
Before the update from BP 1.1.1 to BP 1.1.3 I didn’t get the confirmation dialog before the delete-button took me straight to the ‘Page not found’ error, after the update, I get the confirmation dialog and then the 404. And yes, it seems to be the same Activitiy Stream bug described in the other thread, RSS feed not working either.
You’re not alone in this – I seem to be having the exact same problem. However I don’t even get the confirmation dialog, it’s going straight to the ‘Page not found’ error when I try to delete an activity. We’re still on BP 1.1.1, though. Have you made any progress with this during the last couple of days?