Pathing is fine as I adjusted that prior to trying to firing any of these apps up but they are using relative paths anyway with the emulators and roms all being on the same drive.
I am fairly certain that it was a setting in retroarch but I switched it over to bsnes balanced core this morning and everything still worked. I'm working on PS1 games now using the mednafen_psx core and everything is moving along smoothly.
I think I might run into problems with the PS2 since I can't use retroarch for it but I have found some promising posts about older versions of PCSX2 which can be made portable.
Thanks for the assist !
-Oats