I've noticed on my A500 tablet (Tegra 2) that if I touch the screen while playing with four fingers, the FPse will instantly force close. This only happens during emulation, not in the menus. I am running a leaked official 3.1 ROM, available here: http://forum.xda-developers.com/showthread.php?t=1136900. I also play with a wired Xbox 360 controller (USB).
Actually I just tested a bit more, and there are a couple more details to note:
* One finger tap: No crash
* One finger drag: No crash
* Two finger tap: No crash
* Two finger Drag: No crash
* Three finger tap: No crash
* Three finger drag: Crash after about one second
* Four+ finger tap: Instant crash, drag untestable.
edit: BBCode [*] doesn't seem to be working, I'll just do that ^
Hope this helps. Only other device I have available to test is an HTC Evo running Cyanogenmod 7. I'll test this later. Thanks for the awesome emulator though, definitely a good way to spend $5.