I have installed Linux Mint KDE (the newest Ubuntu version plus also the Debian Version, where I added KDE through synaptic) on my Netbook. As this netbook has a limited resolution of 1024x600 I have set the KDE Taskbar to autohide itself, so I get more usable Desktop real estate. The Taskbar is at the usual position at the bottom of the screen.
Now I have installed VMware's VMware Player (downloaded from their site) and installed Windows XP as a Guest OS. This Guest OS is run in full-screen mode. Also inside this XP guest I have the taskbar at the bottom of the display and in autohide mode. When I move the mouse to the taskbar so it appears, and try clicking at one of it's buttons, nothing happens. If I make the taskbar double size, It takes clicks. If I move the taskbar to a side of the display, clicks work. I have also tried clicking on functions in other windows. If those buttons are at the bottom of the display, also those buttons won't accept clicks.
If on the Mint host I change the taskbar to always be visible, mouse-clicks work in the Guest! This doesn't matter if I use the debian based or ubuntu based of mint. I have also tried it with "Desktop Effects" turned off, and then I don't have the issue. On Mint I also tried this within Gnome with the taskbar setup the same as in KDE, and there I don't have the issue, But within Gnome Compiz doesn't seem to work properly.