Maybe there just happened to be a change of command that took place in the time between those two episodes. One officer's tour of duty at SB11 was done, and the new guy took over. Happens all the time in the real world, no reason for it not to in ST as well.
Indeed, that's the simplest explanation.
With every opportunity available to distinguish between the redshirt and the goldshirt of SB11, I'm keen on declaring Mendez either a resident fleet ops commander or even a mere visitor, one with a personal attachment to the case (he's on first-name basis with Jim Kirk, but more significantly, Kirk is on first-name basis with Jose - unlike was the case with Commodore Stone).
Kirk knows all the goldshirt Commodores pretty well, and they know him, but the redshirts are more distant. Is it just the shirt color that breeds formality?
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