I'll start with the obvious. Make sure the Nook is powered off and that the micro SD card is all the way inserted before powering on.
Try booting into the regular Nook 1.3 and then insert an SD card and make sure the Nook detects it. If not try going to settings and then mounting the SD card and see if that helps getting it to recognize the card.
If it doesn't detect the card and you can't mount it, try a different SD card. If you can't get it to read or mount that card either it would seem you have an issue with the micro SD card slot.
The version of the stock ROM should not make a difference since the Nook never sees it if you boot from a card. I would suspect the card slot is bad or not seating properly.