I had the same problem, I was freaking out cause i thought i had a virus from downloading Misao.exe. I decided to check my taskbar and saw "Facebook, Steam, Utorrent, AOL" all that junk. so i closed out of them all. After closing all running programs, i rebooted my computer, came on these forums asking why my SKSE wont work, as I am typing "WTF WHY WONT SKSE WORK" Skyrim randomly starts itself and is running better than ever. So if any of you are still having problems, i recommend restarting Steam, and any other applications you have in your taskbar. then restart your computer.