What did you do when you offered to "fix" the firmware?
On a rooted stock Nook HD+, I ran the app, and it offered to "fix" the problem in firmware. I said yes, and rebooted as recommended. When the Nook OS (Android 4.0.4) finds something it doesn't like (eg, a detected modification to /system or its children) when it boots, it reboots again. After eight reboots, it will reinstall the original factory image and do a total data wipe as well.
BEFORE IT GOT TO 8 REBOOTS, I stopped it and inserted a bootable microSD card
(yes, most Nooks will boot from an SD card!!!) with CM11 on it, so I have access to the internal flash from CM11. Now, if I were to know what you did as part of your "fix", and can undo it via the booted CM11, that would be nice, and I can avoid the forced factory reset of the internal flash.
FYI: I use SuperSU as well in the rooted/stock Nook OS, and I have to do a little "dance" in /system/xbin anytime SuperSU updates the SU binary: I move the SU binary to a "hidden" folder and symbolic link to it. The Nook's modification test of /system and its children, ignores symbolic links and "hidden" folders (those with names beginning with a period). This is not a problem; it's just info for you.
Edit: OK, from looking at the timestamps of directories and files, it appears that you added the file /system/etc/permissions/android.hardware.usb.host.xml, especially since that filename is not in the factory load. It contains:
Code:
<permissions><feature name="android.hardware.usb.host" /></permissions>
I moved that file to my "hidden" folder, and symbolic linked to it. That fixes the native Nook OS booting/rebooting problem, and causes an app that previously complained about the lack of USB host mode, to not complain any more. USB host mode still does not work, but that's not your problem ....