Brian Duff posted a fix on his blog for cotvnc which is described here:
Here's the main description of the problem in his words:
I have a dual monitor setup at home: one 1600x1200 secondary display,
and the 1680x1050 display built into the Mac. In all, that's 3280
horizontal pixels spanning just under a meter, which is freaking sweet for
development :). Sadly, however, when you make the VNC window full
screen in the secondary display, CotVNC blacks out the primary display.
His patch was further enhanced by another person and the entre patch is
I'm uploading a copy of the patched RFBConnection.m file which includes
both of these fixes.
This fix is what made cotvnc entirely useful for me, as I use multiple
displays, and was completely annoyed by this bug!