Okay... another update...
It seems it wasn't my manual futzing causing the problem as much as I wasn't giving my system enough time to see the SD storage.
I am now having almost 100% success by:
1) Connecting my reader to the system and waiting for the system to see
both storage locations
2) Starting Calibre and waiting for Calibre to see
both storage locations.
3) Play!
Sometimes it can take up to 20 seconds for everything to settle. My laptop is older so it's not a speed demon. I was starting Calibre too early so things hadn't settled and the SD card wasn't being seen.
All well now!