I must add that each album folder contains a .cue file created at the time of ripping the CDs.
That's it, right there.
MC has .cue support. It has imported the files, as well as the cue file that references them.
Pick a duplicate and check what MC has in the filename field for each. You should be able to see from there which is the actual file reference, and which is the .cue entry. It's been a while, but IIRC, the .cue entries have a comma, or maybe semi-colon followed by a number, at the end of the filename.
Your library is brand new, so, you could clear it and start again without much loss other than time
Before you do that though, you probably want to turn off .cue file imports...
Go to "Options > Library and Folders > Configure auto import"
From the list of folders you see there, select the one that contains your music, and click the "Edit" button to the right of it.
Expand the audio section and uncheck cue files.
OK your way back out.
This action will only prevent future imports, it will not remove existing cue imports from your library.
Auto import settings are library specific, so, if you simply clear the existing library, you'll be good to go from there, however, if you create a new library, remember to disable cue files in auto import settings before importing anything.
RE: "Freezing"... MC has been known to handle well over a million files, so it won't be that. My guess would be, as your library is new, it's likely busy building thumbnails, but without more info (probably best in a new thread) that really is, just a guess.
-marko