I had this same problem with both vnc4server and tightvncserver running on Wheezy and both SSVNC and tightvncviewer in Squeeze. The ‘fix’ of clearing the shortcuts works, but this is not a fix, it is a workaround.
What is peculiar is that the shortcuts were set to "Super+Up" and "Super+Down", not just "Up" and "Down". Therefore the problem seems to be that either the VNC client sends extra modifier keys together with regular keypresses or the VNC server interprets the received keypresses as if the modifier key was pressed. This is not the first time I noticed this with VNC. I also regularly use a VNC connection to a Mac OS X machine and in very specific circumstances, typing "i" or "r" will actually trigger shortcuts as if the 'command' key was pressed. In another specific situation, pressing the space bar seems to do nothing. This makes working in certain applications a frustrating experience. Alexander
