Moving this to the Winamp Bug Reports forum, seeing as it's related to the pmp plugin system in the Winamp program and not actually anything to do with the Winamp For Android app.
I've not personally used the auto Sync feature for years, I just select the files in the Playlist or ML that I want to transfer
and do right-click > Send To > Android Drive X
As far as I know, it can't/doesn't transfer the same file(s) twice, and it won't transfer any files if the metadata (Album Artist, Artist, Album, Track#, Title, etc) is exactly the same.
Could just be a UI bug somewhere in the devices/pmp Sync dialog...