I had that problem with RIN (GB/GBC emulator). I reinstalled it, and most of it worked fine. Make sure Nester J 1.11 is compatible with your firmware too. In my NesterJ some ROMS just don't work at all. Some hacked ROMS like Super Mario Frustration (youtube it) need a patch in the ROM folder. If you have hacked ROMS they wont run due to lack of a patch.