Perfect example...
I just deleted the entire contents of my handheld directory that I use to sync my Podcasts over. So I cleared it completely. I then pulled up the handheld in MC and clicked Sync and it synced over the podcasts that I had chosen in the Handheld's Sync List. All is good. I then navigated away from the Handheld in MC, and then navigated directly back to it. It immediately listed one file as In Queue.
This file, as you can see from the screenshot below, was already synced. It's right there (the duplicates are highlighted in Red). Also, in the list, you can see there are two duplicates already there from the first sync (highlighted in blue). I checked, and the are NOT two files in the actual Podcast listing in MC (though this happens seemingly all on it's own too). It did indeed copy two copies of that file over (one suffixed with a (1) in the filename). The files are identical in file size and in every other way I can figure...
I should add.... The settings for my "handheld" are this:
I navigated away and then back to the handheld, and now it is going to sync a bunch of new files. This time, it did detect (I guess) that the files are already there because it has them listed as "Delete on Sync".