If a file is tagged with both V1 and V2, which has priority?

V2. It's in the FAQ.

Which *should* have priority?

The application has no way of knowing.

I can envision some complex rule-based processing that one could do on the tags at import time, and it would result in a good educated guess as to which of the tags is the good one. I don't think Emplode does it, though.

I haven't tried throwing a dual-tag file at Emplode recently, so I don't know how well it behaves at the current time. I'll have to check that out.
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Tony Fabris