It would have been interesting to understand what happened, but I don’t think this had to do with the server. The CTRL+V you are talking about is handled by the application that is target of the clipboard operation, not by the NX server.
If the copy+paste operation worked by right clicking on the selection, it should have worked even using a keystroke. It is more likely that the problem was resolved by the application restart.
I will close this topic now. Just open a new one if you need to.