Some of the things in Changes to folders are not being detected may be relevant.
It might be interesting to try the debugging mode discussed in there, to see if there's a long delay between the change and the filesystem reporting the change back to Opus. Samba network shares in particular can handle change notifications in unexpected ways (although it depends on the configuration at the other end).
If there is a huge flood of change activity, the debugging steps will show that as well, and it could indicate that there are so many events happening that there is a backlog to process them all. That would not normally happen with just a file copy going on (there may be a lot of events, but not so many things can't keep up), but it might happen if something else in turn is reacting to the copied files and causing even more events.