As Eteocles mentioned it is bloody Sorn's script. I wish he had never written it! Nearly everyone uses it when they first start using AHK and it teaches some really bad habits

remove the ~ before each hot key and it will fix your problems

from the help file under Hotkeys (~ entry)

When the hotkey fires, its key's native function will not be blocked (hidden from the system). In both of the below examples, the user's click of the mouse button will be sent to the active window:
~RButton::MsgBox You clicked the right mouse button.
~RButton & C::MsgBox You pressed C while holding down the right mouse button.
Notes: 1) Unlike the other prefix symbols, the tilde prefix is allowed to be present on some of a hotkey's variants but absent on others; 2) Special hotkeys that are substitutes for alt-tab always ignore the tilde prefix; 3) The tilde prefix is ignored on Windows 95/98/ME