Having had a friend that was one of the personnel that did the inspections of those who administer MEPS eye exams it is more likely that the person administering the eye exam at the base did it not per exact procedures, and given the number of people I saw fail at MEPS, then pass at a MTF/civilian eye doc, then fail during the physical at OCS that makes sense.
The MEPS techs have to follow strict procedures while the ones at the base are supposed to, often they are a bit lax and this goes for more than eye exams. I found after the fact of 2 people I knew that I was stationed with who were deemed qualified for SNA that rec'd a full physical at a MTF that were found to not be qualified for aviation at OCS.