I am using Ubuntu Jaunty 9.04 and noticing this problem.
So far, the easiest fix I found was to run metacity --replace on the server machine.
This kills the compiz window manager and replaces it with metacity which enables vnc clients to run fine.
I am able to notice the changes at runtime, so changing window manager updates the clients as soons as the command is run.
I am using Ubuntu Jaunty 9.04 and noticing this problem.
So far, the easiest fix I found was to run metacity --replace on the server machine.
This kills the compiz window manager and replaces it with metacity which enables vnc clients to run fine.
I am able to notice the changes at runtime, so changing window manager updates the clients as soons as the command is run.
I hope this helps anyone with this problem.