Thanks for coming back to me on this. I'm trying to get into the habit of clearing all check marks at the start of each session, which seems to be a workable solution.
My ideal solution would be to be able to check duplicates between virtual libraries, or exclude certain virtual libraries when running the find duplicates function. For the time being, now that I know what the "problem" is, I can work round it.
Cheers
Deddajay