The Problem is:
from a Autohotkey forum:
"AutoHotkey uses a system-wide keyboard hook to suppress the keypress. In most cases this is sufficient, but there are some specialized APIs which will detect it anyway. If the other application uses one of these APIs, there's nothing that we can do about it. (In this case, remapping Capslock via the registry may be effective, since it changes the meaning of that physical key.) "
Follow this guide to Keyboard Remapping to remap the key directrly via the registery.
Using the following code if you want to remap CAPSLOCK to BACKSPACE. Created a .reg file using a text editor, save and run it, then reboot. Details in the guide link.
Windows Registry Editor Version 5.00