On the nook: from the main menu, tap "My Library" and then "Check for new content"
Other things to check:
Enusre that your nook is upgraded to V1.2; if not you can follow the steps listed
here
Switch your device off and on again.
I have been using the nook with calibre for a few months and it is working properly on all calibre versions from 0.6.37 onwards.