We've chased on this issue a couple times. Mac mini 2012 flicker/black screen issues have been an issue out of the gate with certain display setups even with stock, factory ram.That said - updates - including a couple earlier this year appeared to eliminate these for pretty much all. Not a cop out, but these systems have not been perfect in terms of video stability for a lot of users right out of the gate.
The factory design specs for the memory in this model are 1600MHZ DDR3 CL11 1.35V (Low Voltage). 1.35 vs. 1.5V memory uses a little less power and generates a little less heat. Relatively small difference, but it all adds up.
We have a couple dozen of the Mac mini 2012s in our testing labs and have not had success in replicating the issue. With the information in this thread, going to look at it in a new way + we'll try to get access to a system and accessories that combined create the problem as well.
Since the current issue is with two displays... and with a report that replacing a mini-Displayport cable was a solution in one of these two display configs - I am having our team look at noise today from the video side. The actual mini-Display port cable we use for the one display witht he Thunderbolt unit being the other display may be related to our non-detection of an issue.
And... noise would give reason why 1.5V memory (which is what the majority of memory ships operating at vs. the 1.35V low-voltage Apple has moved to), with the higher power draw could potentially reduce that aspect. 1.5V memory does operate just fine in all Apple's systems with the LV spec, just not what was factory intended.
CL9 is the CAS latency for 1333MHz. CL11 is the cas latency for 1600MHz. CL9 vs. CL11 I do not believe has anything to do with this. 1.5V vs. 1.35V is what we're going to focus on. Further, as a side note - 1600MHz programmed with CL9 latency is CAS overclocked memory. That would be you don't see a lot of it as there is little to gain with overclocking - unnecessary and tends to increase long term fail probability.
From testing and a lot of experience, this two display issue is limited to certain Mac minis and potentially further limited depending on what two displays/cables, etc in use in the config. And in this situation - 1.5V may be the solution to overcome it. From the reports here, that appears to be the case and we're going to be on this very quickly.