if you look in my previous posts, I had the same thing happen to me a few weeks ago. 7060/80E 454. speedo still worked, trans didn't shift.
http://www.gearhead-efi.com/Fuel-Inj...ll=1#post20340
Durning my tuning and programming with my burn 2, I ended up somehow loosing VSS. I also had a code 51 which EagleMark had showed me (it had been there awhile). And I still have this weird datastream glitch.
During this extremely frustrating day of tuning, I could not get the VSS signal back by programming. I thought it was just a flash error because how could it just all of a sudden loose the VSS?
Local autozone had the computer for $99 instock. Snagged it, installed my G3 and flashed a new chip. Bingo, Everything works again.
For some reason I still have my doubts that it was the computer for sure.....but the reman computer did fix my issue so IDK WTF.
This is really really odd that you have the same issue as I just had with the same setup....although you're emulating.