Well, the easiest solution is to just gut the preferred-activities:
Your Nook may ask you once about a few intents, but that should be it.
It's possible that packages.xml got corrupted.
Also, depending on how a file gets opened there may be different filters for mimetype vs. path filters.
If you are still having problems, narrow it down to exactly how you are trying to open the file.
Use logcat and see what intent generates the picker dialog.