So I have a system set up using nested menus, using ShowMenu.

One of the options runs a script attribute, which contains another menu. I've used a on ready to wait for the player's input for the first menu, but it doesn't seem possible to make it wait for the player to finish choosing from the nested menu before running the code contained inside the on ready brackets. Wait sort of works, but it also ends up causing more problems.

Is there an alternative way that I can do this?

It is discussed on this page, right at the end:
http://docs.textadventures.co.uk/quest/blocks_and_scripts.html

Let me know if it is not clear, and I will see how to improve it.