I e-mailed Hypertech with some questions and let them know about my experience with tech support........ Here is their response...

"Caleb

I’m sorry about the confusion must have been a miss understanding on the model year. We all use the same source to find out which products we have available for the different model years, makes and engines. We just recently started supporting the 3.7 liter with our Programmers. We support the 2007 and newer only at this time.
Now we do support the 2006 Jeep Commander with the 3.7 with our Speedometer Calibrator part# 752001. This unit calibrates the speedometer only for tire and/or rear axle changes. Maybe the tech mentioned this so you’d know in case that would help.
The vehicle computer calibrations and VIN are different each year and the Programmer 52001 is not programmed to recognize the 2006 model. I recommend going to our website using this link to enter a product request, http://209.12.144.7/requests.php. We use this list to determine the vehicles we support plus you’ll be notified once available. Thanks

Jim"

I did the product request in the link they provided, hopefully if enough owners would do the same we will get a programmer made for us '06ers.