The only thing I can think of would be to root again or install Google Apps via recovery. You'd want to create a recovery backup first tho, in case it creates a worse problem.
If you want to try this....
Charge your Nook to 100%. The only risky part of this is flashing google apps. The other steps sometimes fix things. It's up to you.
Downloads:
Download
gApps and copy to your sdcard.
Boot into recovery:
Open rom manager, tap the top button, you should get a superuser request, followed by a chance to pic your Nook Color (if you've never done this). Then tap the second button to boot into recovery.
Backup your rom:
Using the up/down volume to change select, "n" button to do the highlighted task and the power button to go back, choose "backup" in the backups menu. When done, hit the power button until you see "install zip from sdcard".
Flash gApps:
(you could skip this step if you want to try everything else first)
Then highlight "install zip from sdcard" and press "n". Find your gapps file and install select it and press "n". When it's done. Press power until you see the above menu again with "advanced" menu.
Clean up some stuff:
From the advanced menu, clear "Dalvik cache" and "fix permissions".
From the "mounts and storage" menu, "format cache".
Then hit power until you see "reboot system now".
Your first boot will take longer b/c of deleting caches. Walk away for at least 5 minutes so you don't second doubt yourself.