Dual Boxing Annoyance

Having an issue when running multiple instances of FFXI on Windows 10 that I'm hoping someone here might be able to shed a little light on. Every time I Alt Tab or mouse click between windows it will quickly repeat the last few button/key presses I used on the previous window before allowing me to do anything. I used to run multiple instances all the time on previous versions of Windows without running into this problem before, so I'm wondering if it's tied to a setting somewhere in Windows 10. I usually play with an Xbox or DualShock 3 controller using ScpToolkit.