Andrew - I've done some more testing and have been able to get Syncdocs to create duplicate folders predictably.
The issue seems to involve folders (or sub-folders) shared with me that Syncdocs is unable to delete in Google Docs (I'm guessing because I don't own them). Steps I followed were:
1. In Windows, I created a new folder in my assigned "My Google Docs" directory (call it 'MyNewFolder') and then a subfolder (call it 'MyNewSubfolder')
2. In Google Docs, I then shared that folder with a colleague
3. In Google Docs, my colleague then went to the shared MyNewFolder and created a new folder in 'MyNewFolder' called 'ColleagueNewFolder'
4. Back on my PC, after Syncdocs had run its course, in Windows I could see that, under MyNewFolder, ColleagueNewFolder was sitting next to MyNewSubfolder - all okay.
5. In Windows I then dragged ColleagueNewFolder into MyNewSubfolder.
6. Syncdocs detected the changes and attempted to mirror a deletion of the original ColleagueNewFolder and then uploaded a new version of ColleagueNewFolder within MyNewSubfolder - both these seemed to be processed okay (no errors in log file).
7. Looking on Google Docs, however, the deletion of the original ColleagueNewFolder didn't appear to have been processed in Google Docs and the folder still sitting there - my guess is that the deletion couldn't be processed as this was a folder shared with me by someone else and not owned by me, or the deletion was processed then the folder was immediately recreated.
8. At first, nothing more happened - however, as soon as anything happened to the original ColleagueNewFolder (e.g. opening the original ColleagueNewFolder in Google Docs) the original ColleagueNewFolder is downloaded by Syncdocs and now sits under MyNewFolder (as well as under MyNewSubfolder).
Hopefully this is clear enough to follow.