More questions than answers.

What steps are you using to connect to your vehicle, and at what point is it failing? It is possible your ALDL is not getting vehicle power, check fuses. Does any other type of scanner or code reader work on the vehicle? I use another program to read the PCM (LS Droid) and just use Tuner Pro to modify it, then use LS droid to load it back into the PCM. I have not used the real-time tuning portion of tuner Pro yet, that is the next step.

I found Tuner Pro to have rather a steep learning curve, but is a pretty capable program. I use a another program called universal patcher to check the checksums before loading it back onto the PCM. There are others here at use PC hammer as well as other programs.

Let us know how it goes,
Jeff