Thanks to all who chimed in. I learned some things today. I now understand a little better how the 2 configs interact. It did help to delete the .cfg files. I apologize PL1, I did not fully understand what was going on. As it turns out, the only games giving me problems were ones where I had tweaked the "this game" settings. I did not even remember I had done it (long, long ago). As a result, MAME ignored the global settings.
I'm all good now, but I do have to re-do any custom mappings I had done in the past, which kind of sucks but I am glad I did not do too many before the switch over.
As a side note: I had set up LEDblinky to use the keymapped settings and when I switched over to joystick button inputs, the buttons would not light. This was easily fixed by keeping the keyboard mappings alongside the joystick button mappings in global. The only pain in the ass is if I customize a game map, I need to map both the keyboard and the joystick buttons, but not a big deal.
Thanks again!