VM Version: 7 and 8 (makes no difference to the success of the cloning)
The way i read the OP - two thirds of the time he has no problems at all.
If that is the case I do not see how it can possibly be rotating his good backups out of existence - unless he has a rotation of one!
I would be manually running ghetto from the esxi cl with a very basic config file for three consecutive days to eliminate as many variables as possible. This would also include using a different destination datastore.
Edit: I would also be upgrading to ESXi 5.1