I just ran into this issue with my two monitors and I fixed it by enabling fullscreen, restarting dcs, and disabling fullscreen.
Are you using any additional software like DCS Device Server?
I have two monitors stacked on top of each other. The top one is 3440x1440 and the bottom one is 1920x1080. I've been using Helios without issue until the update to 2.9.6.
Everything works exactly the same except the HMCS for the A10C. It's getting centered between both monitors. I've tried adjusting the monitor config Lua and creating new ones. Some with the UIMainView and GU_Main_Viewport set to the same width and height settings as the center view and others using Viewports.Center. Any thoughts on how to get the helmet display centered to my main monitor (3440x1440)?