Maybe this is a clue to what is happening.
After months of not having 2 monitors when they were working in the past. I finally decided to purchase a Diamond USB 3 to HDMI adapter and plugged it into the dock. Installed the drivers, and the additional screen didn't work.
Ugh!!!!
When I right clicked on the Desktop and clicked Display Settings, I could only see two Monitors 1 & 3, (i.e. the SP3 and mini display port monitor on the docking station)
I then clicked on "Advanced display settings" located under the apply button.
Even though extra display didn't show up in the identify monitor display window. Clicking the dropdown under Multiply displays, I could see "duplicate monitors on 1 and 2". I clicked it and all three monitors appeared in the main display settings page
and started working. A little rearranging on the screen and all three monitors worked the way I wanted them.
So being the curious type, I unplugged the USB 3 adapter and re-plugged in the mini display port adapter and 3 monitors are working again as they where originally setup, i.e. one monitor plugged into the mini-display port on the docking station and the second monitor
plugged into the mini display port on the surface pro 3.
Hence, it's definitely not a hardware issue or an issue with the monitors.
Obviously, I can't recreate it and I don't recommend buying a USB3 to HDMI adapter, but someone with the issue might try this:
Hook up 2 monitors.
Right-click on the desktop and click Display Settings.
Notice they only see monitors 1 and 3 or 1 and 2.
Click on Advanced Display Settings.
Select the drop down on Multiple displays and see if it contains the missing monitor.
Select the option that contains the missing monitor and see it fixes the issue.