Weird issue here.
I cleared my MC library and imported a backup from my Windows version, without settings (just the library), because it contains dozens of new custom fields with calculated values (an Ode to MrC!), and nice views.
I ran auto-import and let it clear missing files (no protect missing drives). It looked oke but then I noticed double entries appearing for the same files (ie, every song listed twice, exactly the same, pointing to the same file).
I looked at my import settings and noticed I had ticked everything, not just audio (but data and playlists as well).
I simply deleted everything in MC (not from disk

). Reran the import but only audio ticked. Few minutes later, everything is still showing twice, even for albums which don't even have a playlist or cue file.
Basically I got less than 8,000 unique files:
$ find . -type f \( -name "*.dff" -o -name "*.dsf" -o -name "*.flac" -o -name "*.m4a" -o -name "*.mp3" -o -name "*.ogg" -o -name "*.sacd" -o -name "*.wv" \)|wc -l
7379
It seems every time auto-import runs in the background, files get added as a new entry in the database. I ran it manually and now everything is showing 3 times.
Import details:
Library now has 28968 files. Search and update took 7:41.
Imported 9120 new files.
Fixed 413 broken links. (8 fixed, 405 removed)
Updated 1161 files that had external changes.
Failed to import 1 file.
Skipped 123 files (previously determined to be bad).
Has anyone else seen this behavior? What setting would cause this to happen?
Thanks for the help!