I tried it several times here but was not able to reproduce this issue. My guess is that letting GarageSale re-indexing your database might be worth a try. @ilja what do you think?
Can you locate the original listings in the hierarchy in GarageSale? My guess that it has lost it’s parent, and therefore GarageSale does not know where the put the duplicate.
The “Fix Orphaned Listing” option in the Debug panel (hold the Ctrl key during startup) should fix it, but make sure you have a current TimeMaschine backup.