The calibration tool (in "Wacom tablet" the Settings Control Panel) in Ubuntu 14.04 appears to have a numerical bug. It looks like it's using the existing xinput calibration values to help work out the new ones, but that perhaps there's some offset at the side of the screen (or a global maximum value which its truncating at) meaning that every time you use it the pen shifts a little further out of calibration. The error grows with each calibration.
Perhaps someone could point me to the code where the calibration tool takes input and updates the xinput "Area" option for the stylus, and I can have a look to see where the problem is. (Sorry I don't know how to find it)