i had a similar issue using linux. after returning from ydl to gameos, it seems that the bluetooth-stack is down. wether my 2 controlers nor my bt remote were working. the controlers were loaded and worked using usb, the bt functionality went back after switching off the unit on the back.
oh well... it seems im not the only one having problem in v2.41. for the controllers seems to be fine... but the XMB it self is not for me... for example:
when i insert a game disc (BD) and start a DEMO game (Naruto Ninja Storm) after i starting the game. i eject the disc, and return to xmb without quitting the game... and as i see the Disc is still inserted. even I ejected it... and thats not all, the videos on my PS3 seems to be off-sync... cause when i play a video (anime nogizaka haruka) the subtitle itself is offsnynced.
All of these problems show to me after i upgraded...