What is the difference between having folder in the preferences > Library tab monitored, and having a library created from MusicBee > File > Libraries?
Creating a new library literally creates a new .mbl file and a few associated files on your drive. The library files don't care where they are; the location of the audio files in your library is totally separate. Monitoring a folder is a library setting. You can have a library without having any monitored folders. Any folders that are monitored for a library will be included in that library.
I had only the master library monitored. And it seems that adding things to the master library file locations while the portable library was open was what crossed MB's wires. I've added the portable library folder to the monitored folders in preferences as well.
From what you describe, you *don't* want to have both folders monitored by either library, because that will have the same result that you didn't want. You want to monitor only the folder associated with your currently active library.
The portable library also contains straight up doubles, since I copied a lot of files from the master folder into the portable mirror - and then added compressed files created from the .wav's and .flac files in the master library. So when I opened the portable library, I kept getting all the doubles.
If you have a monitored folder, all files from that folder will be included in the library. So if you have duplicates in the folder, they will show up in your library.
The odd thing too was that after creating the portable library, INITIALLY it worked as intended, but then after switching around between libraries and adding new files to the master file folder things got screwy. I'll have an eye on this...
It's certainly possible that a bug exists. I've had separate libraries with separate monitored folders that I copied files between, and never noticed an issue of the wrong files showing up, though.
Like I said, you can have a library without monitored folders. If it would make things simpler, just scan the folders manually from time to time instead of monitoring.
Added: on thinking more about monitored folders and moving files around, it is possible that if you had MusicBee open and moved files belonging to the active library to another location, that MusicBee would still keep them in the library in the new location. Once a file is in your library, it will stay there as long as MusicBee can keep track of where it is.