Try using Process Monitor to see what Opus is doing during that time. Is it reading the same file, or set of files, over and over or something like that?
Also try disabling all plugins and the other things suggested in the FAQ on issues that happen when reading particular folders. It's possible that the problem isn't synching but is something going wrong when the results of the comparison are displayed.
You could test that theory by viewing the two folders in Flat View mode to see if anything goes wrong. View -> Flat View in the default menus.