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Thanks. That's very strange behaviour. As far as I know, the client will only ever apply a duplicate pair relationship if you work through the duplicate filter or apply it manually on a selection of thumbnails, either through that menu or with a shortcut. I have no auto-dupe tech yet.
As a side thing, there is some transitive behaviour, so if A is a dupe of B, and you then set B to be a dupe of C, then A will be duped to C also, but of course this needs the triggering B->C relationship set in the first place, which it sounds like you are not doing. Also, duplicate relationships will survive files being deleted and re-imported, if that could be happening here.
If you can figure out a way to reliably reproduce this situation, or you gather any other information that would help me track this down, please let me know.