It could be related to this :
^x::^c Makes Control-X produce Control-C. It also makes Control-Alt-X
produce Control-Alt-C, etc.
It is taken from the AutoHotkey Help Pages.
What have you done is : Control-W produces Alt-W.
You said you wanted to use Ctrl+W to close tabs.
If Ctrl-W produces Cltrl-Alt-W because it produces Alt-W and Cltr-W at same time, it means that the application has time to catch the internal signal.
It might be because the application is looking for the BIOS keys or either that that auto-hotkey doesn't react fast enough.
I remember that there's was an option to put a autohotkey to sleep for x-time or make send more signals at the same time.
Sending more signals at the same time will prevent the Key from the Bios to reach the application. AutoHotkey will always translate the stroke so the application will read the right keys/AutoHotkey signals only.
I hope my long explanation helped you.