First of all, hi, I am new here. I wanted to register to the forum for giving my insight in this flicker issue. We had that problem at work. I own myself a Mac Pro 6,1 with D300 as well.
For giving a background:
At work we had a total of 7 Mac Pro 6,1 - 5 of them with D300 and 2 of them with D500. (I never ordered a D700.)
The D300 were connected through mini DP to DP to 2 monitors: one 2k monitor and 1 HD monitor
The D500 were connected through mini DP to DP to 2 monitors: one 4k monitor and 1 HD monitor
(my personal D300 was connected through mini DP to DP to 2 monitors to a DCI 4k monitor with no issues)
However, we had a problem with two machines at work, both of them D300, with a flicker issue.
All the machines at work were brand new. Indeed, we contacted Apple about those two machines, and I should recognize that Apple was “a bit” frustrating.
So, I found that, in our case, the problem was the mini DP to DP cable!
In our case, the “cheap” cables were causing the issue. Since we changed to the Startech mini DP to DP and to the Eizo mini DP to DP “PM200” cable the issue completely disappeared in those machines.
Maybe not all the issues comes from there, but in our case that was the problem. I hope that helps.