Update: 1.42 also fails, and its NOT an SLI issue.
I'm also getting a Direct Draw error, it dissappears fast though:
idirectDraw7: setcooperativelevel failed
And yes, dxdiag says everything is all right.
Turning off and turning all acceleration options back on failed to, as did re-installing Direct X.
Re-installing Direct X did make the setcooperativelevel failed go away at least, but ZSNES still minimized when it goes to full-screen.
SNES9x 1.51 and 1.50 also fail with full-screen mode. Emulator auto-minimizes
EDIT 4: ISSUE FIXED
Control Panel -> Display -> Settings -> Advanced -> Troubleshoot -> Uncheck "Enable Write Combining"
Write Combining speeds up the writing to the display, and was the issue causing the full-screen errors. Disabling and restarting windows should fix the problem
Another restart broke it again. I'm looking into it
EDIT 6: (Fixed for now) (im so banned
16 bit color mode MUST be enabled. That seems to have done the trick...