I am having the same issue, but cannot get it rectified by alt-tab to windows and back. Here are some details.
Setup: Intel core I7 -4820k, 16 GB Ram, twin GTX-780's (3GB), with three ACER 27" monitors and 3 ACER 23" touchscreens, running Win 8.1.
Everything works, including touchscreens, until the mission loads. Then the mouse and touchscreens no longer function. The Warthog HOTAS joystick and all buttons, etc. work. The graphics function perfectly on all 6 screens.
If I use one monitor, or configure any 3 monitors in surround mode, then the mouse works fine in all phases of the simulation. If I use three touchscreens in surround mode, the touch functions, but cannot be calibrated due to Windows limitations, not DCS.
Any advice would really be appreciated. I am new to DCS and know that I am pushing the limits with the setup. I suspect this is a multi-monitor problem with the software. The question is if there is a work around?