I have this issue as well. See also http://www.gameex.info/forums/index.php?showtopic=1108 5.45 has no problems but in 5.46, the emulator menu item is gone, despite emulation settings. Used a default .ini and simply changed 1 emulator entry to point to the right paths and it is still the same. edit: Also, in 5.45, I couldn't get it to scan subdirectories to find my ROMs.