If I turn the InputActions auto-generated class into a singleton by adding the following block of code to it, and then referencing it via the instance instead of making a different copy of the class for each action map scriptable object (which was my previous implementation) it fixes the issue.

public static InputActions Instance
{
get
{
if (instance == null)
instance = new InputActions();
return instance;
}
}
private static InputActions instance;

I'd suggest adding a singleton aspect to the class, or some variation on it to make this easier. I could of course have my own class specifically to store this seeing as it could be more closely related to my implementation, but I feel like having it function as a singleton would be beneficial overall.

Long story short, the problem was that each action map was referring to a separate copy of the InputActions class, but by having them each refer to a single instance this problem is solved.