I'm working through an issue writing calibration with my new MPVI2. I had found a few posts with somewhat similar symptoms but nothing that helped to get the car back going. I stumbled on something that worked so I thought I'd post the story in case it will help someone else.
It connected and read the stock tune no problem (GM E67 ECM). I made some changes to the idle tables and went to write it back up. It connected, went through the initialization steps, erased, and then on write it failed after few percent and said timed out. I tried it again and it failed right off and again said timed out. Many more tries, lots of cursing, same failure and at different points in the process. Dead car of course.
I submitted a ticket to HP but it was Saturday and I took the risk and kept working at it. I tried three different computers (and every USB port on each one), as well two other USB cables I had. I tried the released and beta VCM editor, tried the stock tune, different sequences of power up and device connections, no change at all. Still failed at random points in the write process. I did finally give up and waited for HP to reply.
HP got back to me Monday and by Wednesday they said it was a communication error, and they suspected my OBD2 wiring. Suggested I try a bench harness. I didn't really agree since it's an unmodified GMPP harness and I had connected other devices to it before without issue. But, it wasn't impossible so I gave it a try. I made the bench harness and still had the exact same issue. I happened to find a short 6" USB C to A cable yesterday that I had here for whatever reason so I tried that - and boom! It wrote flawlessly on my bench setup. I'm not going to push my luck by verifying with more write attempts but it did read no problem, both on the bench and back in the car.
So, it seems to me there's something sketchy with the USB communication on the PCM and it's going back to HP Tuners. At least the car is back running in the meantime! I'll post an update when I get it resolved with HP.