The issue occurs in the second level of nested dictionary.Iterating over nested dictionary and editing the key by popping the old key and entering the new key. The next iteration, at the second level of nested dictionary, then skips the second key in dictionary and continues from the third key. In debug mode found that on editing the first key, the new memory allocated points to an address that lies between second and third keys memory address. 

Let me know if some other information is required. I am attaching the python file where I successfully reproduced the issue.