Basically when you press Alt it activates the window menu (indicated by a small underscore), so when you then press any other key it opens up a dropdown if it is a valid combination (example Alt+F drops down file menu, Alt+E does the edit menu etc) or it gives the default windows beep if it is invalid.
I've tried using autohotkey in various ways but the most success I managed was switching the Alt key off altogether but that isn't what I want, I just want its functionality where it goes into the window menu removed but still work in other ways.