You did not mention if apart from the atmega and radio module, there is the 4MBIT FLASH-MEM chip on any of them?
Also, the RFM69 modules, what types are they on each of the Moteinos? That may make a difference, since over the years the HW/HCW modules have been manufactured with a different RF switch chip (the 6 pin SC70 package).
To really compare apples to apples, all these Moteinos should have identical configuration, and ideally without a radio module, or if the RFM69 is present - either from the same batch (this is impossible) or of the same type (ideally RFM69W or CW which don't have that RF switch).