I'm using 4.01 M33-2
The only problem I see in the snes emu is that sometimes the screen will black out if you keep switching between fusa and the emu menu. You just have to blindly activate the fusa menu disable and re-enable.
But it doesn't happen all the time for me. Could be a few things... What version of the emu are you running?
I'm currently using: SNES9x TYL 0.4.2 ME
I was using 0.4.2 (not the ME version) and it seemed a little more buggy to me...
Though I have found that certain SNES games just don't work with FUSA... immediate crash after loading it up.