I have also been struggling with an autocommitted issue and have found something that can cause this but is not obvious on first look and is intermittent.
It may help you with your problem, it may not.
Two entities with a 1-2-1 association. Delete behaviour is set so that Entity2 will remain if Entity 1 is deleted but Entity 1 will be removed when Entity 2 is deleted.
Within a MF - entity1 is created and has the commit flag set to false – (autocommit object)
Same MF entity 2 is created with commit flag true and attributes set. Association to Entity1 is also set. – (normal object)
Further MF activity continues along with a change action to Entity1. Attributes are set in here and so is the association to Entity2. A page is then opened with this Entity which has a standard Save and Cancel button.
User clicks Save and immediately logs out – autocommit error is logged and Entity 2 is lost.
I have a 3rd entity behaving in the same manner as entity 1 but without the initial association to Entity 2 being set on the Create action. This object never suffers from the autocommit situation.
So the result is that by setting an association on a normal Entity, even with the commit flag set, using an autocommitted entity for the value can cause your normal Entity to be lost. (This only happens for me if the user logs out soon afterwards.)