OK I think maybe it was a glitch. I couldn't replicate the issue again with 5 games I tried. Maybe it was a mame program on one of the games that caused that. Of course I wont be able to find it. LOL
Still trying to figure out how to set up parameters for each core in retroarch. I figured out how to call a Mame program in a game and it worked beautifully. I think I would call a a core in retroarch by selecting retroarch n the edit and then in the custom command line I would write for Arcade -L "cores\mame_libetro.dll" since this is the core I would like to call. I understand I do not need that on this line because this is how I set it up initially in Launchbox. If I want to call another core, I would set it up in retroarch by loading core, and then saving configuration name. Then I would use that config name if I wanted to call another core in retroarch. This is a bit tricky. Am I on the right track. I understand there is a lot more to do with CHD files etc but I'm not getting into that right now.