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Ok, so I have tried with a Fedora 24 Live USB based on Fedora-Workstation-Live-x86_64-24-1.2.iso. All displays worked as expected at 3840x2160. After that I then re-installed using that Live USB and no surprise UHD worked as expected, however then I updated the system (about 1000 packages) and after that it was back to 1920x1080 for both of the external monitors.

Hence, I do not think there is a hardware problem, but rather a bug in either the drivers or the display server packages.