It sounds a lot like some focusfollowsmouse is causing or could be used to fix. Odd I know but if you are using it and your mouse hits a non-hidden taskbar or random window, it can cause weird effects. If you don't use it clicking another window and a slow response time to the key can cause undesireable effects. In order to help further we would have to see your script. Just make sure you remove passwords and usernames from your script if you have them in there. Enclose the script in code tags to maintain formatting, and help out the forum mods so they don't have to do it for you.