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I had similar problems with my custom keyboard layout that uses option for some keys. I fixed this as well as paste problems with the following patch:
http://www.olofsson.info/cotvnc-misckeyboardfixes.patch

This patch is much less invasive than the other one available, and works in all applications such as firefox on Linux. I have only tested it againts a linux VNC server so it might break other servers.

Binary available at:
http://www.olofsson.info/Chicken%20Of%20The%20VNC.zip