My guess is that the problem lies in a common misunderstanding of inheritance.
Let's say that you have a note Memo that already has some key attributes:
But you want to inherit Key Attributes from the prototype MyPrototype
Now, if you let Memo use the prototype MyPrototype, it will inherit values from its prototype except when it has its own values. And in this case, it already has a value for $KeyAttributes, and that overrides the inherited value!
What to do? If you're using QuickStamp, you can simply click the arrow button to use the inherited value. Or, you can delete the key attributes you don't want; when you next load Tinderbox, it will straighten out the inheritance. Or, you can use the action (or stamp)
which means, "use whatever value this note inherits, or use the default value if there isn't a value to inherit." This, for example, is what your agent probably wants to do after assigning the prototype.