Perhaps trying to sort though two or three different folders confused the database operation?
If you have overlapping names such that MC would want to copy 2 or more files to ONE file name in the destination, that might happen. If they do NOT overlap, then it shouldn't matter I wouldn't think.
One more weirdness: I have several instances of almost all of a CD's files copied to my new hard drive, but one (or two) files not being copied). After a couple of subsequent attempts I ended up dragging and dropping the file within Mac OS-X, then importing into the MC Library, then using the Rename/Move/Copy utility to rename all the files for that CD to be consistent and keep them together.
One of the good things that will come out of this exercise is I'll have my file names cleaned up and will be able to locate things on my hard drive and everything should also be arranged within MC the way I'm used to organizing things with actual CDs.
I've found this to be true. MC is as much of an organizational tool as it is a player. In fact, using MC is a really great way to get a handle on where your files are and what they are. Then it gives you the opportunity to organize them, on disk, in a very structured fashion. It's quite satisfying to someone like me to gain control of my media collections so I can really know where everything is.
At some point you might find that you need to do some external organization (with Finder or another tool). This might mean that you just want to start from scratch with a fresh library and reimport everything. If it's not that drastic, you don't have to. I'm just throwing out the idea that it might help you depending on how your media is laid out on disk.
When you are doing these kind of disk organization tasks, including figuring out WHAT you have and WHERE it is, it's VERY useful to use the Audio > Files view. I can't remember exactly which fields that view has by default, but the important one is DISK LOCATION. Drilling through your collection and then seeing where everything is on disk can really help. You can drive the process either direction: Start by looking at disk and see what files are there. Or start by looking at albums and artists and see where the files for each are located. This is another good tool in the toolbox for having a nicely organized collection. Both inside MC and on the disk. I think both are important.
If you have specific questions about RM&C, or about using a files view, or even building your own CUSTOM files type view, I recommend you start a new topic about it. That way we can give you focused help. Sometimes people won't answer posts there there are several different questions together. But they will answer several different posts with one question each.
Good luck! (and I sincerely mean that even though I type it a LOT in my replies).
Brian