Very weird. But something similar has happened before.
The mistagged file question is a good one. Common with TV Shows that identified as Movies, or visa versa. Being Audio I can't imagine a file being identified incorrectly though, particularly as it has already ben imported into another library and works.
Is there any information in the Recently Imported Smartlist?
If you use the Files View under Audio, can you find the missing files? Drill down to the location and look. If you find a missing file, check the tag windows to see what Media and Sub Media Type it is.
BTW, what format are the files? MP3, FLAC, etc.
Are they the same as all the good files?
Will the file play using other Windows software, rather than MC?
Give me an example file name of a good file, and a bad file. In fact, the full path and filename of both, plus the same for the computer where the bad file works. Could path length be an issue?
Also, try running Auto Import manually rather than using Drag and Drop. Humour me on this one.