Check the preferences for the device driver in calibre to ensure that PDF is selected as a format that the device supports.
You can check one of two ways:
- With the Nook attached on the Device drop down (the little arrow besides the word Device in the top menu) select Configure this device and ensure that PDF is an allowed type
- With the Nook NOT attached select the Preferences menu, then head to the Advanced section and click on Plugins. Within the displayed list expand the Device Interface plugins option and select the Nook Device Interface (1.0.0) Communicate with the Nook Color, TSR and Tablet eBook readers entry. Ensure that PDF is an allowed type.