1st, make sure you have backup of your sites and settings.
i'm not exactly sure of your situation, so i'll go w/ what i understood.
once you uninstall flashfxp, try to uninstall that 2nd entry in add/remove programs. you'll probably be able to remove it. if not, then try to re-install flashfxp into that same backup folder and uninstall both entries.
if that doesn't work, plain registry editing will do the trick
