Hiding windows with Hide Window Hotkey

I use Hide Window Hotkey to hide my WoW windows with a press of a button, but it doesn't work when they are opened through ISBoxer. Does anyone know how to get it to work or another program that will do the same thing? Is there something in ISBoxer that will do this? Thanks.

[lax]

If you focus something other than a WoW window before doing it, they should hide fine