I've seen this before.
You copied a Library (in Windows Explorer) instead of using MC to create a clone, or restoring from a backup. Probably because you wanted to make a new Library and use your old one as a starting point (next time, be sure to choose Clone as described below instead). In any case, something of that sort happened, which caused the Libraries to have matching GUIDs. Then they reference the same settings in the Windows Registry, and have matching AutoImport settings (and other Library Specific settings). It is fixable.
There are two ways, depending on if you are picky about the exact folder name where the Libraries are stored on disk.
1. Open the Library Manager in MC (under Playing Now in the tree).
2. Select the first Library that has the problem, and choose Clone Library on the right-hand side.
3. Pick a new location for the Library and save it. Give it a name like "My Library Duplicate".
4. Repeat steps 2-3 for any other "affected" Libraries. (Technically, you'd only need to do it to one of a "pair" to break the link, but I've found once you get this messed up, better to start fresh with totally new GUIDs.)
5. Delete the original copies of the Libraries.
6. Rename the new ones back to match the original names.
If, instead, you're picky about what folder (on disk) the libraries are stored in, here's an alternative method:
1. Open the Library Manager in MC (under Playing Now in the tree).
2. Load the first Library that has the problem, and make a backup of it.
3. Delete the Library from MC (switch to the other Library that has the problem, in the meanwhile).
4. In Windows Explorer, find the Library's folder on disk, and delete or rename it. Make a new, empty folder with the proper name for the new "copy".
5. Open MC back up. Create a new, blank library, and choose the folder you just made.
6. Restore your backup to this new, blank Library. DO NOT choose to restore settings, only the Library itself (or you could end up with the old Libraries re-loaded, since the Library Manager's list of libraries is included in the backup).
7. Repeat 2-6 above for any other affected Libraries.
You may need to set up your Auto-Import Folders from scratch with these methods.