If you have already unbound your Key Bindings as outlined here, then perhaps you’re running into the Windows/Numpad issue mentioned here - assuming your macros are bound to numbers 1 thru 6 on your numpad.
The latter issue is something I ran into with my previous play style, and one of a few reasons why I decided to change things up - to get all of my Key Modifiers (SHIFT/CTRL/ALT) to work as intended.
Since moving my spells next to my movement keys (as shown in the video) I have not experienced a single Key Mod problem. This is my recommended solution (changing play styles), but probably not something you want to hear as it is very difficult to do. I can sympathize because I know how long this process can take - I fumbled through it for several weeks. Of which, it was all worth it in the end.
I hope you find an AHK solution or something less painful instead, and if you do maybe you wouldn’t mind sharing your solution with the community.
This is something I have considered and may release in the near future.
Until then, good luck! 