Do you power it completely down, or leave it in a standby mode (power down - hold power button until it asks you if you want to turn off the Nook - standby - push the power button momentarily)?
It sounds like a software-type issue to me... I just had that happen with my phone - the phone said that the battery was nearly discharged when it had been recently charged. I tried charging it, but it wasn't showing that it was charging. I turned the phone off and then on, and it showed a nearly full battery - and when the charger was hooked up, it showed the battery being charged.
That sort of thing can happen with portable computer devices.
When this happened to me, it was the cord. If you bring it into the Nook desk at your local B & N, they can check your cord and let you know if this is the problem. Since mine was still under warranty, they ordered a new cord to be sent to me, and it's been charging normally since then.