Here's the script to disable windows start menu, but allow modifiers, it works as intended:
LWin & vk07::return LWin::return
I want to disable Fn+Win key, because it's opening windows start menu.
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The answer depends on your keyboard and computer.
If you suspect that the combination Win+Fn generates a special key, you may find out what this key is by using the procedure described in the AutoHotKey article Special Keys.
Another method for tracking what that key-combination is doing, is by right-click on a running AutoHotKey script in the tray-bar and choosing "Windows Spy".