Nook auto shut off after factory flash and reset.

I recently decided to go back to complete stock. I wanted to see how a factory stock rom would deal with the battery issues and others I've had. That's where the problems really began. I followed the instructions in a current thread. I used this thread years ago to root my nook without a problem. My Nook HD+ this time would not boot from any SD card. It did not matter what image I used or what method from the mentioned thread. The SD cards are good though. I stupidly did a factory wipe/reset in CWM, mostly because I had tried everything else. I knew not to do it, but I had tried everything! My Nook would stay on the Caynoboot after this. I finally got a flash to work using the old method and CWM 6028, but this time it hung on the Nook screen. After fighting this for a while, I finally got the stock recovery and stock rom to flash. Great, it's working again as it should. The problem I have now is if I leave it alone for a bit the Nook will shut off. I can power it back on, but sometimes it takes a couple of tries. I tried to charge it this morning when the battery went down to 6%, but I could not use my Nook charger. It would shut off or start to boot past the Nook screen and then shutoff. I'm typing this now and my Nook is charging fine through my computer. Has anyone experienced the auto shutoff when leaving it alone? It's totally annoying, but it functions fine other than that. All of these problems came to life after going back to stock root. Personally, I don't feel like starting over again. I'm to nervous that something will go wrong.

My thought is this relates to all the known battery problems the Nook has. CM might eliminated some of the obvious though. Mine started 3 months after I bought it years ago. It was part of the reason I went to CM10 at the time. I thought maybe the factory rom was the issue. Do you guys think the auto shutoff and normal charging method issues are battery related? I don't think it's a hardware issue. It could be the way the rom was finally flashed, but I would expect more problems other than the above. One thing the factory rom did fix was the Nook shutting off on almost any flash video. It was always random, but this has not happened since going back to stock.