OK, what I found was that if I get the settings how I want, then SAVE the settings, then EXIT... the NEXT time I start the program, I can see the settings are saved while RCS64 checks all the com ports for devices. After that process is complete, and it has found my APB, Pit-Pro, and Scorpius dongle, then Auto-Pit is unchecked and greyed out.
If I exit and restart RCS64, the Auto-pit option is STILL greyed out during the com port check process. It would appear that my setting is being overwritten for some reason, some how, during that com port check process.
No matter what I do, save or not save the settings, when I start RCS64, the auto-pit option will end up disabled, and grey. The only way I can enable it is to disable Pit-Pro, enable Pit-Pro, then Auto-pit is available, and I can enable it.
Here's a screen shot of my main page, in case that helps at all.