Is it possible that the first file didn't appear in the list on both sides? It uses the list content to know which files already exist, so if the file was added after you did your listing FlashFXP wouldn't know about it.
I turned on DGFS and tested this setup and in every test the files are skipped as expected.
The same size comparison is done whether you have DGFS enabled or not, however the method used to get the size is different. when DGFS=1 then we look at the size in the file list, otherwise we issue SIZE to get this value.
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