I'm not on the latest CM11 nightly (I'm on 0118) so this might not mean much, but whenever I wake up my HD+ with the power button I hear an audio pop or crackle. It is just for an extremely short instant. I usually have my volume turned off so didn't notice this before, but it only does it if my volume is not off. I didn't have it turned up all the way either, just somewhere mid-range. I saw an earlier post where someone was getting an audio pop with an immediate reboot, this is not happening to me, just an audio pop, I have had no lockups, crashes or reboots at all with CM11. It works great.
Also, I have had no screen flashes with CM11 but this seems oddly familiar. I have 2 HD+ nooks and one of them had screen flicker months ago right after I rooted it and put CM10.1 on it. I think it was on my wife's nook and was annoying her enough she didn't know if she liked the nook or not, but luckily it went away, probably with a new nightly ROM and she has loved it ever since. Now, her nook is still on 10.2 because I have been waiting for CM11 to get a little more stable (I don't like to mess with her working setup).
And regarding your wife's NOOK set up: I wouldn't mess with it either. I went back to the CM10.2 Snapshot M1, installed 8x8 trim kernel and installed Tablet UI and it is ROCK SOLID. Seriously - I love CM11 and its snappyness but the reboots, flickering issues made me go back to this stable set-up. We will just have to wait for a stable CM11.