I have a very similar situation and i would recommend looking into whether you can connect the monitors to both the dock and the desktop video card.
In my case it was necessary because my screen is 144hz gsync and my dock does not support that, so I needed a way to get that to work.
In theory, my desktop has 3 screens attached. Screen A (144hz) with DP, Screen A with HDMI through the dock, and screen B (just your basic 1080p60hz) with hdmi through the dock.
All you need to do is identify which "screen" is the affected screen(s)'s output through the dock and disable it in the OS and it will work out.