Mystery Solved!
Well I've continued to investigate, and just in case anyone else ever experiences this sort of thing, I thought I'd just make a note here:
- I use a Linux based Buffalo Terastation to store my FLAC files
- I use an Apple Airport Extreme to establish my home network
- I use an Microsoft XP pro PC to run Media Center
I had been using a couple of networked external USB drives to host my FLAC files while I waited for my Terastation to arrive with personal effects from overseas.
Seems likely that my "lost" files were down to illegal characters being used in some file names, together with some filenames that were over 27 characters long. I've juggled my FLACs between the Terastation and the apple formatted USB drives, and I've recreate my MC library quite a few times.
I had been having trouble sync'ing the USB drive to the older Terastation, so yesterday I upgraded the Terastation's firmware from 1.06 to 2.12 (or something like that) - this allowed the Buffalo to handle longer file names, and then ran some scripts on my Mac laptop which went through my FLAC files on the Terastation removing any possible illegal characters like: ",\#$?..., etc (for some reason my Mac could see files that Windows couldn't).
When I re-ran MC library import, 400 "new" FLACs were found - so they had been there all along - just invisible due to naming issues.
I'm not exactly sure whether this was a Linux, Apple, or Windows issue, but if you find you're missing files from both your hard drive and your MC library - and if you're running a mixed environment - maybe you should check your file naming by accessing your hard drive with its native OS.