That's pretty much what happened to me: it would turn itself on, including wifi, and stay on and drain the battery.
however, I just shifted to the latest nightly from here:
http://download.cyanogenmod.com/?device=encore and it runs fine now. (I guess I have 253) It's not coming on when charging, and the battery is not draining, so I'm pretty happy.
(Except for the fact that I thought this was an upgrade, not a new ROM, and so I didn't back everything up first. Which meant I had to replace everything on the Nook. D'oh! I won't make that mistake again!)