I Experienced this kind of behaviour over a VPN connection, and it turned out to be that the VPN lost contact (some sort of timeout?) and reconnected itself. If I was doing something in NX that needed a licence check, it would freeze up for a while until the VPN was running again.
After a while I figured out that it happened due to the VPN reconnected, so I simply started a command window and typed:
ping -t license.server.ip.adress
And then I let it run minimized, pings every second, but makes sure the VPN won't timeout, it solved the problem for me, but I ping the server 3600 times in an hour ;-)
(unfortunately the ping-period in windows cannot be altered, but a .bat file with a loop and sleep should be able to solve that)