Hi, as many people here, i also had a problem with StrokeIt icon permanently displaying in Windows 8 taskbar.
I found (by accident :) ) a solution which is suitable for me and i belive it could suit even others.
You just need a global action which minimizes window with command "Windows - minimize". If you start gesture that activates this command on StrokeIt icon in taskbar, then it minimizes it to tray. Usually the icon won´t show up again when Windows retarts but sometimes it does and you need to minimize it again.
Hope this help. forinti