it could be 2 things. 1) it’s not in the AHK script to be able to use modifiers. 2) Could be that the in game Key Binds for SHIFT and ALT have not been unbound. Check the keybinds in game and let me know 
also grab the script from here: What is MS and how can I change it? Answered (With working AHK script you can use with Modifiers) - #13 by comicus this script allows modifiers