EG:

SQLSTATE23000: Integrity constraint violation: 1062 Duplicate entry 'node-2572-0-0-und' for key 'PRIMARY'
SQLSTATE23000: Integrity constraint violation: 1062 Duplicate entry 'node-1834-1834-0-0-und' for key 'PRIMARY'
SQLSTATE23000: Integrity constraint violation: 1062 Duplicate entry 'field_collection_item-340-6872-0-0-und' for key 'PRIMARY'
SQLSTATE23000: Integrity constraint violation: 1062 Duplicate entry '5-delete own news content' for key 'PRIMARY'

I've tracked this down to not every field in a compound key being used to sort the table when batching. This means that there's no guarantee of the order of records for the whole table, and therefore records returned in the first batch show up in the second batch onwards. This causes the records after the duplicate in the batch to be discarded.

I've fixed this locally. Will upload a patch soon.

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rupertj created an issue. See original summary.

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Adding patch.