I can't speak for Tom, but as a long-time user, I would suspect Tom will not release any more updates to the script, since, as you can see, it is several versions of ACR behind, already.
The version of ACR makes a difference to the script because it has to zero out all the sliders and new versions of ACR can add new sliders. If the script warns it is not compatible and you choose to run, anyway, then it doesn't zero out the sliders (like the contrast curve to linear is the main one), so it can work, ok, but to have it work exactly the same you have to zero out the curve and make sure other things are, yourself, before running the script. I don't know how compatible or not the script is with CS4 since I quit using it before upgrading. I would suspect you're running out of memory or something about OpenGL isn't quite up to par and running the same thing over and over is running out of resources. You could try it with OpenGL turned off.
However, the main recommendation is to not use the script, anymore, because ever since Adobe Labs released the DNG Profile Editor, which lets you create a custom camera profile from a Color-Checker with up to two color-tables the same as the Adobe profiles have, not just a set of slider values relative to an existing profile like the script does, the need for such a script is diminished, and Tom seemed to have abandoned it, some time ago, probably as soon as he know Adobe was working on the DNG Profile Editor months before it was released. While the name DNG Profile Editor includes the term DNG, it is really for any type of RAW file, so don't think you have to convert to DNG for it to work.
The DNG Profile Editor is available from:
http://labs.adobe.com/wiki/index.php/DNG_Profileswith more information, here:
http://labs.adobe.com/wiki/index.php/DNG_Profiles:Editor
The beta 2 camera-profiles are obsolete as these profiles come with Photoshop and Lightroom, already, so don't download and install the beta profiles, just the profile editor beta.
The two ways to use the profile editor are to create a dual-color-table profile with the CC photographed in 2850K and 6500K light sources, OR create a single-table (or both tables the same) profile that is specific to whatever color light you are balancing for.
I have a dual-color profile I use for most things where ACR/LR interpolate between the two profiles based on the WB of the image, and then a few specialized profiles for particular lighting situations (such as a studio setup or sunset) that I want as good as possible. The hardest part about creating a dual-color profile is getting the WB of the lighting exactly 2850K and 6500K. I don't have any calibrated light workstations so I had to just take pictures in various incandescent and hazy sky situations until the WB was close and then used the two closest shots I had.
If you insist on using a script like ACR Calibrator, there may be ones from Rags-Gardner or Tindemans that are compatible, so you can Google for those.