You likely need to re-start VNC on both ends. i.e. when you say "restarted VNC", you probably just mean the client. But what about the other end? You likely need to re-start that end too.
The root cause is likely a conflict. Many apps spy on the clipboard when they shouldn't. And many apps are not forgiving when they go to open the clipboard and can't. Robust ones will retry, others will simply not anticipate a failure and then they get fouled up and need to be restarted. Could be VNC, or it could be another app that's "listening" to the clipboard viewer chain, where it is obligated to pass along notifications to the other apps in the chain. If the notifications aren't sent, then VNC may not even know that there has been a clipboard update.
