As indicated, in my case, the client version is also MacBook with El Capitan OS with NoMachine version 5.1.44. Regarding the server in my case, the server is “NoMachine Terminal Server Subscription” version 5.1.24 on the Linux platform.
I have the same version and I have been observing the same issue. Most of the time, I have about a 50% success rate on copy and paste. I guess it is virtual desktop. The applications are anything on a MacBook Pro (late 2013), El Capitan.