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Are other keyboard keys sent to the windows session as they should? I've seen it happen in certain fullscreen games, and it's usually because I've managed to hit alt-tab to change the input focus without sending the new window to front. Just a thought.
Actually, no, they're not. I've checked the VNC list archive and others have the same problem and have had since the middle of last year. I can't find a solution though.
And while I'm thinking, here's another thought: have you tried the KDE vnc client? The one called Remote Desktop connection in kde 3.1. It's a lot better then the standard vncviewer. Plus you get a nice "exit from fullscreen" button you can click, while all keypresses go to the remote session (including ctrl-alt-del :)
No. How do I start it? -- "...our desktop is falling behind stability-wise and feature wise to KDE ...when I went to Mexico in December to the facility where we launched gnome, they had all switched to KDE3." - Miguel de Icaza, March 2003