I upgraded my PS3 to the 3.50 firmware, and my PC to the 10.10 Ubuntu version.
It works without any trouble on my side.
There’s a new trace in the emu process traces (“Unknown feature report […]”) but it doesn’t seem to cause any issue. It seems the 3.50 firmware sends some more bt requests. Ideally the sixaxis emulator should respond to these new requests. It’s added on my task list.
If you meet problems, please report them.