I am experiencing this same issue.
three Asus 144's
xfire r9 280x, previously 2 7970's.
connected via 2 mini display port to Display Port, and dvi-d to dvi
Both sets of cards have done the same thing to me.
When the system crashes or in some cases from a cold boot, the dvi port will only allow 60 hz. I have to unplug the mini-dp's, reboot, replug, and all says 120 hz again.
I setup eyefinity and it defaults to 60, but allows for 120, 144 even since they go that high.
Now Windows says it's 5760 x 1080, but my windows and my internet are all kinds of zoomed in. Only my icons and the task bar look normal.
Trying to play Grid Autosport is all kinds of zoomed in too. The resolution shows correctly, but it is definitely NOT. If I play in "windowed" mode, the game looks correct, but once I turn it to full screen, it looks very zoomed in.
BF4 has the same effect...
Eyefinity is so very awesome when it works, but it sure has it's headaches...