Autohotkey per emulator scripts don't work as expected

[Former user]

Many AutoHotKey commands don't trigger when a game is launched but can be triggered by a keypress e.g.

run, Notepad.exe 

doesn't work but

a::
run, Notepad.exe

works fine, the same is true for other commands like:

Send 
Process
WinActivate
MsgBox

There might be some other that I haven't tested.