I've successfully run CUIT automations for about a year without this problem. I use the Microsoft Environment Viewer bundled with Microsoft Test Manager and Visual Studio 2013 to connect to the machines in a SCVMM/Hyper-V lab environment. Then I kick off the automation, minimize the environment viewer, and work on something else while my tests run.
For thousands of test-runs, my "local" mouse has been unaffected by the automation script running on the virtual machine(s), but that changed recently after I set up a new lab environment containing 4 desktop client VMs. When I run tests on the new lab my pointer moves around my own screen--even after I've minimized the automation window.