[Tom Wyrick]

I, too, can confirm this issue with a new Mac Pro with dual D500 video (doubt that matters though).
As soon as I upgraded to OS X 10.9.3, I lost my third display. I’m using 3 identical 27″ LG monitors running at 1920×1080 resolution. One connected directly via the HDMI port on the Mac Pro, one via a Mini-DP to HDMI passive dongle/adapter, and the third via Apple’s $99 Dual link DVI to Mini-DP adapter.

This especially irritates me because I never ran more than 2 displays before, until I invested in this new Mac Pro. That’s when I decided I may as well splurge with it and get a third matching display screen, and a triple monitor VESA mounting bracket to put them on. That’s when I discovered the nMP had the limitation of requiring one of your connections to be active vs. passive if you want more than 2 displays, so I went out and spent the $99 on the dual-link DVI to Mini DP contraption. Now, only a few weeks after getting that all going — I’m back to 2 monitors again anyway!

I did file a bug report with Apple, BTW. We’ll see how quickly this gets fixed ….