Well I have figured out at least one of the things causing this - I'm still going through old drives and pulling Media from them onto my new PC, so I have a number of discs ripped as FLAC files.
I use ALAC now, so I have been using dBpoweramp's conversion tools on these files - it's a context menu item that completely automates the process of converting, renaming & moving the files to my music directory in the structure that I use with MC, and sending the source files to the recycle bin.
It seems that if the files take a while to convert, auto-import is picking up on some of the changes before it's finished, and even if they were picked up in a single batch, there are often at least two or three tracks per album that are skipped by the audio analyzer tool.
I don't want to import the FLACs where they are and convert inside Media Center, because I have ended up with corrupt files when doing this,
it is "unsafe" in how it handles file deletion during conversions, and is a multi-step process unlike dBpoweramp's converter.
I suspect that the same thing is also happening when simply moving or copying files from another drive, causing it to import the file in batches, and skip the analyzing some of them. (I haven't been able to test this out though)