Posting for future reference...because by next week I will have forgotten.
When I tried to connect I got the RR USB device not found message. I could connect the FlashScan scanner to the RR and log. If I tried to flash through the FlashScan I got the bootloader rejected/PCM locked message.
Seemed like an issue with the RR and FlashScan drivers. I tried uninstalling/reinstalling all USB devices and even tried installing the RR before FlashScan as suggested on here with no effect on the problem.
I wondered if there was a conflict with the USB/Serial adapter driver I had installed to connect to my LC1s for a firmware reflash, as the RR is also USB/Serial. I had issues getting that adapter to work as well. There were no ports showing in the Device Manager when the RR was connected.
I used FTClean to clean any references to FTDI drivers off my system, connected the RR and specified the RR drivers for the reinstall, then connected the FlashScan and specified the EFILive drivers. Everything is back to functioning properly now. Will probably have to go through the same process if I ever need to use the USB/serial adapter again.
So, if anyone has similar issues, ensure that you use FTClean before reinstalling your USB devices. Just following the update driver or uninstall/reinstall process may not work.