AppleTV updated their software to 2.3.1 (with very few noticable improvements) which also seems to have broken Boxee.
But the fix is pretty easy, just re-apply the patchstick again and everything on Boxee will be well again (except for the fact that Hulu still is blocked on Boxee). After the patchstick has be applied, user logins, media sources, preferences, etc. will be just as they were before the upgrade.All of your settings and media will still be there.