10.9.3 kills third monitor
The setup: 2 x 30" Cinema Displays connected via dual-port mini-DP to DVI adapters, connected to thunderbolt ports, and 50" TV connected to HDMI port, in new Mac Pro. All three monitors were working on 10.9.2, only one Cinema display and TV show up after update. Mac Pro has dual FireProD500 cards, 32 GB RAM, 12 cores.
Not sure if this is isolated to new Mac Pro's: older models with two mini-display ports and DVI to HDMI adapter may or may not still work.
Had to restore back to 10.9.2 to get all three monitors working again. Maybe they would work with mini-DP to DP cables? Not sure, have no way to test.
More users with same issue:
Mac Pro, OS X Mavericks (10.9.3)