Since i upgraded to Parallels Desktop 4 3522, the Parallels tools are not working as expected in Ubuntu. Before upgrading the VM was off, not suspended. I have deinstalled the Parallels tools and installed the new ones, but i have to force restart several times before being able to click inside the VM window even in full screen mode, and the desktop will not update its size to the window size ... MacBook Pro C2D 2.33 Ghz / 3 Gb RAM / Mac OS X 10.4.11
Try installing the tools in the VM when X is not running. Updating X11 files while it is running can cause all kinds of odd behavior...
I have the same trouble here, but the most surprising thing, this bug didn't exist at all in the previous beta 4 of Parallels that I found more stable and usable than this final !