Ok, I think I figured it out. For the OTA channels, I didn't prioritize a tuner, but a tuner was prioritized for the STB 'tuners'. So, it looks like since I didn't set the priority tuner set for the OTA channels, it chose the STB tuner. As soon as I set a prioritized tuner for each OTA channel in a 'combined' channel grouping, MC chooses the OTA tuners first.
Thanks for your help,
Alex