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[BartMan01]

Decided to start messing around with stacks on my audio files.
Chose one of my concert DVD's as a starting point since they have DTS, AC3 and PCM tracks.
On my hard drive I have the following files for each track:
Original DTS
Original AC3
APE (from original PCM)
MP3 (from APE - just built as part of this test)

I know all 20 tracks were in the library to start with, since my first step was to create MP3 files from the existing APE files and all 20 files have MP3 files on the HD.
Steps I took:
Converted APE to MP3 (delete original and update library options unchecked).
Imported the folder to get the new MP3 files in to the library.
Manually stacked some of the files.
Selected the unstacked files (other than the ones I am having the 'dts = data' issue with) and used 'Auto stack by filename'.
When I noticed the missing files, I 'unstacked' them thinking maybe MC had just incorrectly stacked them with another group.  I started with tracks 1 - 20.  Tracks 1, 2, 3, and 20 were excluded from my stacking.  Now I have tracks 1-8 with all 4 files in the library, track 14 with just the AC3 version in the library, and tracks 17-20.  Tracks 9, 10, 11, 12, 13, 15, 16, and 3 of the track 14 files are now missing from the library.  I am using my 'All by location' view scheme that has no exclusions or data type filtering (1:  Location(root), Genre, File Type; 3: Only 'populate tree' is checked; 4:  No filtering).

When I look in the directory, the files are there.  When I import that folder (and yes both 'ignore' options are unchecked and all audio file types are checked) it imports 0 new files.

[BartMan01]

I just deleted from the library every file from that directory.  Weird thing is that the directory still exists in my 'All by location' view scheme - with no visible files.  Reimporting the folder just puts me back to a partial list of files.  It is like the library has the files, but won't show them to me - like they are part of a 'stack' that is broken and invisible.

[BartMan01]

Finally got the files back by renaming the directory - letting MC see the files were missing and drop them from the library (even though it wasn't showing them) - renaming the directory back and reimporting.  Lost all my AC3/DTS tags in the process but I got my files back in the library.

[park]

I have reported a similar issue for my photos. The missing photos are not stacked, but like I had been playing with stacks a bit. Maybe I stacked them at some point.