I have two external disk that I keep in step. After a major overhaul, the sync involved a lot of changes, and I found that when it got to the delete part (I'm using delete mode with subdirectories) it would say ready for recycling, then stop - no error or anything. By syncing successfully individual subdirectories I determined that it was the inclusion of one with > 5000 files to delete which caused this problem. When I manually deleted some of the indicated files, bringing the number of differences to 1000, opus sync'd fine.
I should have said - Vista Home Premium - fully up to date and Opus 9.1.1.7
This is probably something GPSoftware will need to reproduce themselves to fix.
I'd try contacting them with the same details at first but if they can't reproduce it just by creating a sync which deletes a lot of files then they might need more information.
For example, it might depend on the exact sync settings plus knowing all the filenames + dates and folder layout of the source and destination. (You can get Opus to generate text files with the details of everything in a folder via Tools -> Print Folder. Within the Print Folder dialog there's a flat-view option which makes it include details of subdirectories.