FWIW...

Mid 2011 Mini server running 10.9.5. I have been running two displays for years with no problem. An Asus and a Samsung. The Asus was connected using an HDMI > DVI adaptor cable.

When reconfiguring my system, I changed the Asus cable to a straight HDMI cable and am now experiencing the above issues on that monitor on a system that DID work. Same OS, I only changed the cable.

I will obviously go back to the DVI cable but thought this may shed some light for others. Yes, it ***** that Apple is so typically silent and unresponsive. I'm a Mac user for 24+ years, and I'm over thier crap. My Windows 7 machines scream with very few problems.

vett93, this adapter you mentioned has a lot of people giving it a 5 star review as a solution to their Mac Pro multiple display issues (look at the reviews at the bottom). I just put in my order for one for my Acer H236HL monitor.

One person said that you need to have an "active" connector for each monitor. I'll see if just this one adapter fixes the issue, and if not, I'll get an additional adapter (for the second display ASUS PB278). I'm not sure which model of adapter to get for my second (ASUS) display because it exceeds the quality of the adapter you mentioned (it has 2560x1440 resolution and your adapter only supports 1920x1200). I noticed your approved adapter list has other styles of adapters such as Dual Link or HDMI, which allow for a larger resolution. Are all of these adapters acceptable?

I honestly don't know any of these terms (Active, Dual/Single Link, etc) so I wanted to clarify which adapter to get. Hopefully the one I ordered will fix it, but I wanted to get the inside scoop while all of this research is fresh on my mind :-)

Update:
The original adapter I mentioned did not solve the issue on it's own so I decided to get an adapter for each monitor. I got two different kinds because they have different resolutions; I got an HDMI adapter for my higher resolution monitor.

It may be too soon to know for sure, but ever since I have been using both adapters I have not had to restart my computer once because of this issue. Most of the time the monitors work just like you would expect, but sometimes they do that flickering thing where it can't figure out if there are two monitors or one. A little annoying, sure, but it figures it out if you give it a few seconds. I've had it set up like this for about two weeks and I'll let you know if it stops working.

Accell B087B-006B

http://www.amazon.com/Accell-B087B-006B-DisplayPort-Single-Link-Certified/dp/B00 4071ZXA/ref=lh_ni_t?ie=UTF8&psc=1&smid=A…

Accell B086B-008B-2

http://www.amazon.com/gp/product/B00DOZHL82/ref=od_aui_detailpages00?ie=UTF8&psc =1

update: This did NOT actually fix the problem. Started happening again. Also that hdmi adapter had the additional problem of flickering white pixels.

My 2 month old late 2013 Mac Pro started to show the problem since last week with Yosemite 10.10.3, and it got worse by waking up not even one display on. ( I have 6 monitors, one TB, 4 display port, one displayLink USB), initially I didn't realize the Mac woke up already so I have to hard reset every time, later on I found the Mac Pro was reachable thru other local computer as the share function is on, I can even SSH to it, the only problem is no display is waken. Only work around under yosemite is to reboot, but with 50% chance success, in fact I have to boot multiple times too to get all monitors up, I'm surprised this is not thoroughly tested in apple, why should people buy a 6 TB pro without apple even testing connect 6 monitors? So frustrated that I can't even use sleep, tried all kinds of setup in pmset with no effect, it woke up randomly sometimes reboot with a error message, sometimes mac just on but no display on like I mentioned. Searched high and low and found there's a lot issue with the sleep/wake problem, on all mac platform! Seems such a fundamental function works like a crap in Mac, worse than PC!

Just found this thread and I wanna share that I rolled back to Maverick and so far so good, at least I can put the Mac to sleep and wake up with monitor on now, sometimes one or two monitors won't wake but by using "detect display" in display preference usually wakes them up again. I can't confirm 100% it will be working as it's only been a few days since I downgrade. Will report if it stops working.

10.10.4 available today, 30 June 2015, supposedly with fixes for some display problems.

Just tried and same old problem, waking up on its own with no display signal. Downgrade to 10.10.2 now. The issue started on 10.10.3.

Re: Yosemite 10.10.3 Second screen big problem

Correction, I have to downgrade to 10.10 to get rid of the sleep/wake issue. Now the only problem I have is iTunes will crash/reboot the computer upon open, after about 5 seconds, even with fresh installation of OS. Fine I can live without iTunes, but really is this the apple quality?

just updating that the problem has been solved (for now) on my computer for months now since I installed Yosemite.

I have an ASUS PB278 that has always worked fine with the Mac Pro. The second display, Acer H236HL, would often loose connection on and off driving me crazy for many months of use. I bought a Mini DisplayPort to DVI-D Single Link Active Adapter (up to 1920 x 1200) which I think helped the problem but never fully solved it.

Once I upgraded to Yosemite, the problem went away completely. I haven't had an issue since. I am currently on 10.10.3.

Not sure if that helps anyone, but thats my specific circumstance with the issue.

After updating my Mac Pro late 2013 to OSX El Capitan 10.11.2 (15c50) the above described problem started - before everything was fine. 

My only workaround not to lose my unsaved files is to leave the monitor off for a while and then try again, until it sometimes manages connect to the monitor. - and sometimes it doesn't sleep at all.

Did the problem for any of you return after the latest update?