E11000 duplicate key error index while stopping the Balancer

Our MongoDB Backup script (python) disables the balancer using:

self.config_db.set_lasterror_options(fsync=True)
self.config_db.settings.update(

, { '$set' :

}, True, False, True)

About 30% of the time, the following exception is thrown:

06:41:18 Traceback (most recent call last):
06:41:18 File "/opt/XXXX/bin/mongo.backup.py", line 398, in <module>
06:41:18 balancer.disableBalancer()
06:41:18 File "/opt/XXXX/bin/mongo.backup.py", line 47, in disableBalancer
06:41:18 self.__setBalancer (True)
06:41:18 File "/opt/XXXX/bin/mongo.backup.py", line 43, in __setBalancer
06:41:18 self.config_db.settings.update(

, { '$set' :

}, True, False, True)
06:41:18 File "/usr/lib64/python2.6/site-packages/pymongo/collection.py", line 411, in update
06:41:18 check_keys, self._uuid_subtype), safe)
06:41:18 File "/usr/lib64/python2.6/site-packages/pymongo/connection.py", line 831, in _send_message
06:41:18 rv = self.__check_response_to_last_error(response)
06:41:18 File "/usr/lib64/python2.6/site-packages/pymongo/connection.py", line 778, in __check_response_to_last_error
06:41:18 raise DuplicateKeyError(details["err"])
06:41:18 pymongo.errors.DuplicateKeyError: E11000 duplicate key error index: XXXX.m_generics.$id dup key: { : "11f1952c-55b0-474b-950e-f03c54d538b5" }

After a few attempts, the script succeeds in disabling the balancer.
Any ideas of how to handle this? Does this point to a bigger issue (are there really duplicate keys somehow?)