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I remapped my wheel mouse for Windows Media Player. The remap works unless I change to full screen mode. Then AutoHotkey does not recognize it as the active window, and the remaps don't work.

How to fix this?

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F8 and F9 will modify the volume, and will work in fullscreen mode as well. I'd map your mouse wheel to send those keys instead.

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It is mapped to F8 and F9 for Windows Media Player, but it only works when it recognizes that Windows Media Player is the active window. – Phenom Dec 29 '09 at 15:50
    
You can use controlsend to send it to the WMP window if it exists: autohotkey.com/docs/commands/ControlSend.htm – John T Dec 29 '09 at 16:27

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