Because AHK is just sending a quick keypress: down,up.
When you press (and hold) Up on your main, your alt gets sent:
Up for a split second, regardless of how long you hold it on your main. Your alt won't move very far.

You need to be able to just send the "keypress down" event to the alt when you press Up, then send the "keypress up" event to the alt when you release the Up arrow. Look at my script for F1 - that's how I do my formation spread - you should be able to use something similar.