I can only offer a couple of generic thoughts here. Before installing the new Vega cards did you uninstall the other cards from device manager? Did you then run DDU from safe mode to clear the old driver? Then install the Vega with the latest driver and once it ran okay then add in the second card, often times you can then reinstall that same driver over the old one if need be. That would be my plan of attack on this. Also before any of that, is Windows fully up-to-date with all updates even optional ones? Also do you have the latest bios and firmware for your motherboard? Looks like F23d is the latest bios for your motherboard if that isn't what you have. If that isn't working after that I would wonder if it is maybe an issue with different brands of cards and their likely different bios. I know there are some good mining forums out there that would probably have some advice too. You might throw this question out there as well. I would also ask the companies that made your cards, Powercolor and MSI.
I have solved this problem myself.
This is what I did:
1. I uninstalled Afterburner
2. I unistall the radeon drivers using DDU.
3. I shutdown the PC.
4. I put back both radeon VEGA 56 GPUs into the motherboard.
5. I started the PC, waited until it's stable, and then installed the radeon graphic drivers.
6. I tried to give the graphics some mining loads. They work stable.
7. I stop the load.
8. I install the latest version of Afterburner.
9. I tried the respective GPUs parameter settings in Afterburner.
10. Tried giving them load again. They worked without problems.
11. As a bonus, I tried adding an RX 560 card on the last PCIE slot. It works.
So the problems were either bad drivers of afterburner.