I have verified that the MegaObjects returned by root.getObject(metaClassID) and instance.getClassObject() have the same ID and Name, so the error appears odd. These are the questions that arose from this:
Why does the first code throw an error where the second succeeds?
What is the difference between instance.getClassObject() and root.getObject() with appropriate ID?
How can I work around this behaviour in Java if I only have the MegaObject instance and need to get its MetaClass Object?