I suggest you stick with it and expect the problem will be identified and resolved. It does seem to be a strange one, so that may take some time.
I may be missing something from what's already been done, but I tried this simple test. I added some test files to my music folder using folder names similar to those you've mentioned, and then ran Auto Import. From the summary...
Imported:
D:\Audio\Test, genre\Artist - (Year) Title [ed.ition]\Test 2.flac
D:\Audio\Test, genre\Test 4.flac
D:\Audio\Test, genre\Green, Grant - (1964) Talkin' About [2010 Music Matters 2xLP 45 RPM Hires]\Test 3.flac
D:\Audio\Test, genre\__Coltrane, John\Burrell, Kenny;Coltrane, John - (1958) Kenny Burrell and John Coltrane\Test 1.flac
My test files are copies of an existing, tagged file. Thinking that might have an impact on the results (I'm don't know how), I stripped the tags, deleted the files from the library, renamed and re-imported them. That worked as well.
My Auto Import configuration is to include D:\Audio, so this was not a test of the folder issue that's already been identified. I did try adding these folders (and C:\JUKE-BOX 2\Black, soul, disco\Jackson, Michael - (1982) Thriller [Japanese First Pressing]) to the import configurations, and could not reproduce the "folder not sticking" issue. So I assume this was fixed in build 103 ("Fixed: Path names with semi-colons in them could be problematic").
Could the issue be with the files themselves? How are they named? Is MC having a problem analyzing them, and tagging them as Data rather than Audio? You can check this by displaying Media Type in the Recently Imported playlist, or by looking for the files in the Documents section.