Unwanted Duplicates

I dragged my AppleMail Inbox into EF and then pared it down in EF to several hundred messages. Some time later I discovered that I had over 3,000 messages in my EF Inbox. Many appeared to be duplicates. I can discern no differences in comparing these duplicates - title, tag, from, to etc all the same. My preferences box for allowing duplicates is unchecked.

Any suggestions appreciated.

The recommended way to import from Apple Mail is to press the capture key, not drag and drop.

Please see this thread.