I use FCEUX for Windows in Wine because the SDL version lacks a step debugger. In Ubuntu 14.04 with Wine 1.6.2, I open a ROM, open Config > Input, and change port 1 from Gamepad to Mouse. Once I click OK, I get a crash. Terminal tells me it's an unhandled null pointer exception: "page fault on read access to 0x00000000". I can get a backtrace if you tell me which interim build to use.
I think I was getting the same crash under windows. Could you check if it's fixed with this change?
https://sourceforge.net/p/fceultra/code/3214/
Crash no longer happens under FCEUX r3218
Considered duplicate of: https://sourceforge.net/p/fceultra/bugs/726/