I’ve noticed that my Intuos 3 Tablet Pen does not go all the way to the bottom edge of the screen in Zbrush. Top, left and right are fine, but when i place or drag my pen to the bottom of the tablet surface, the on-screen pointer stops about a half inch short of the bottom of the actual screen. I have also seen this in my 2D paint program. I can’t access the bottom portion of the window or get to the Windows task bar without alt+tabing to the desktop. I have no issues in others software, just these that actually use the features of the pen. i’m am running Zbrush 4 in Vista x64 and my tablet has the most current drivers.
In your Wacom Tablet Properties, on the ‘Mapping’ tab, is your tablet area and screen area set to Full?
Yes, it is set to Full. I have also tried the proportions check box but get the same result.
Also, I recently upgraded to 3DS Max 2011 and have seen the same problem in certain situations. Most of the time it is fine and I can go to all edges of the screen, but when I perform an action with the Graphite modeling tools that will bring up the Caddy, such as Extrude, from that point forward the bottom 1/2 inch or so of the screen is not accesible with the pen. A restart fixes that. It is more annoying in 3DS Max because there are actually buttons and things down there I need to click.
I’m having a similar problem with my wacom intuos 4 and Zbrush4, but only when I’m using one monitor it has issues going to the bottom of the screen, when I’m using two there’s a whole host of other issues (which i posted about here http://www.zbrushcentral.com/showthread.php?t=94371 but havn’t had a reply yet). In a weird way it’s good to know its not just me… 
Problem Solved.
It seems to have been an issue with the driver. I thought I was using the most current one, because I had alot of issues before setting it up. But somewhere along the way Windows decided to insert its generic driver. So now I am back up and running with the “real” driver. Yay!