If that helps then it could be that something is flooding or delaying the change notification system (in Windows) and having a knock-on effect on when Opus processes the changes.
You can check using DebugView and turning on the notify_debug and shellchange_debug settings mentioned here. (Turn no_external_change_notify off again as well.)
If you see a fast, constant stream of changes going by when nothing much is going on, then that may be part of the problem. Or, if you don't see notifications for the operation you just did until a while after it has completed, that may also explain things.