What would cause a loss of traction control that was permanently burned?

I recently replaced the TB and EGR gasket due to some significant vacuum leaks. I reset the PCM by pulling the negative after getting everything back together. The car runs perfect but the traction control was permanently turned off with the tune, but now I have to manually turn it off every time I turn the key on now. What gives?

And also, I'm not sure if it is related or not, but just recently my speedo and odometer stopped working and I got a code for the VS sensor(VSS) circuit malfunction - P0720. I replaced the VS sensor with a new one but it did not fix the problem with the speedo/odo.

I've heard that the VS sensors on these are a common problem, but what are some other common problems that make the speedo/odo stop working?

Going up.

Thanks Mike. I was wondering if there might be a common issue with the gauge cluster itself on these, but when I get a chance to get under the car I will definitely take a look along the trans harness.