I may have become slightly cynical living in Latin America for the past 19 years, but the initials on the upgrade list were not the only clue given by the OP in the OP. He also stated that the seat he was originally assigned in coach, 5F, became available sometime between before the flight and after the flight. 15 of 16 booked and checked-in in First. No one on the upgrade standby list. It is starting to look like a duck, and even Polly Ana would start to get suspicious. That a FA handled the upgrades is the nail in the coffin. Add all these other circumstances to the mathamatics, and it is pretty clear what happened.

I would further guess that with a 2-1/2 hour WX delay, that CO was deadheading crew down to SJO so as not to have to delay 1485 the next day back to IAH due to crew rest requirements. I would guess that this group may have been favored by their co-workers.

I think that CO should step up and fix these things, and if they don't when they get caught, should provide better compensation. A FF program is suppose to work both ways. A customer will be loyal to the airline, and the airline will provide perks. This customer was being loyal to the airline, but one of the airline employees denied him his perk and gave it to someone else. In this case the GA seems to be involved also, so at least 2 employees are bending the rule in detriment to their passengers, ...oops customers.

I think a BF oneway upgrade certificate would be fair compensation.