are you using the serial or USB cable hookup?
i have used many of these controllers (about 60 of them). the only issue i have had was with a weird calibration issue on maybe 2, i had to enable the 25 point advanced calibration and calibrate it with that one. i only think the xp install comes with it, i don't see it on my vista install at home here, but it's on all our xp installs. i believe the file to manually run it is called "elova25p.exe" i think you can just pull the file out of the install pack and run it. for some reason the units i had, came with a strange linearity table programmed into them.
some of the older driver versions had an option to WRITE the info directly to the controller or just load at the start via a config file. it was to keep the firmware from getting corrupted. i think since those versions it gets written by default.
it seems to "work" no matter what when I start the computer, but the cursor does not jump to or follow my finger when the calibration is lost.
does it match your left/right movements okay but inverses the up/down movement? (or vice versa) or does it just not line up properly (but the up/down left/right are correct directions)
these controllers are very susceptible to static discharge. often even if the ground cable is properly attached, a static-y finger can fry the controller through the overlay. (this has happened on maybe 5 controllers. once 3 times in the space of a few months due to a broken ground wire.)
as another option (assuming you are using the 5 wire flat ribbon connection this will not work with the 4 wire connector.) just unplug the cable and flip it over and plug it back in. (it will work either way) This reverses the horizontal and vertical lines. do a new calibration and see if it sticks.