When copying to system clipboard and it is unavailable due to some other application have locked it, DbVisualizer tries 5 times until giving up. The following should be in the DbVisualizer log (Tools->Debug Window) when this happens:
Could not acquire system clipboard after 1 tries. Will try again...
Could not acquire system clipboard after 2 tries. Will try again...
Could not acquire system clipboard after 3 tries. Will try again...
Could not acquire system clipboard after 4 tries. Will try again...
Could not acquire system clipboard after 5 tries. Will try again...
Could not acquire system clipboard after 5 tries. Giving up!
Uncaught exception: java.lang.IllegalStateException: cannot open system clipboard
So the problem is that there is another application using the system clipboard. If the problem persists, try closing down tool by tool until it works.