Well, I have no idea what was wrong in the first place, but a fresh install onto a new flash drive seems to have solved the issue.
I reconfigured the system, added the drives back into the array (with the known good parity box checked) and then reestablished my VMs using their existing disk images.
All applications were functional, so I crossed my fingers and rebooted. Everything came back up with the correct configuration, the array was online and all VMs were running.
Played around a little more getting everything back in order, then tried another reboot. Again everything came back up as it should.
I don't know what was wrong, but I'm going to call this closed if not outright solved.
Thanks to everyone for their suggestions to work through this...
-John