Have you tried firing the shutdown by holding the power button for 6-10 seconds? Then hit the power button again and you will see the Surface screen if it shutdown properly. When mine start to misbehaving, forcing a shutdown and then rebooting usually corrects everything. Worth a shot.
I had the same thing happen to me. I did a refresh and it didn't fix it, I did a complete wipe and restore and it did. Then I went back in and started tweaking like I did before and the bug came back. It was a change that I did after reading it in one of the forums that trashed it again. I undid that change and it all started working again. I wish I could remember what it was that caused it, but look at some of the tweaks you have done.