This is still an issue as of 2014-06-20 on 3.13.0-29-generic in Ubuntu 14.04, however I have now upgraded to a single 4K monitor and a Haswell CPU, so I won't be able to test any further possible fixes for this issue.
One thing of note though, is that when X came up on 3.13.0-29, the second monitor did display the correct content for a few hundred milliseconds. The image would flash in and then away very quickly, as the screen turned to a giant solid colored area.
Running "xrandr --output HDMI1 --crtc 0 --output HDMI3 --crtc 2 --right-of HDMI1" on log-in did make the second screen usable again.
This is still an issue as of 2014-06-20 on 3.13.0-29-generic in Ubuntu 14.04, however I have now upgraded to a single 4K monitor and a Haswell CPU, so I won't be able to test any further possible fixes for this issue.
One thing of note though, is that when X came up on 3.13.0-29, the second monitor did display the correct content for a few hundred milliseconds. The image would flash in and then away very quickly, as the screen turned to a giant solid colored area.
Running "xrandr --output HDMI1 --crtc 0 --output HDMI3 --crtc 2 --right-of HDMI1" on log-in did make the second screen usable again.