I was thinking the same thing as many others - we've been on the PG, booked our own air, went a few days early, and never told anyone at RSSC when to expect us. We never did this, but it would be not at all unreasonable to drive around the island, take a ferry to/from Moorea, or do any number of things on embarkation day, as long as you arrive by the stated boarding time. I speculate that the person who was asked to check if all booked passengers had boarded made a human error.
In Papeete, as I'm sure in most embarkation ports, you can check in and then leave the ship and walk around town, have a crepe at the roulottes, whatever. It doesn't sound like that's what happened, but if that were the case, the system of scanning the key cards should have indicated that passengers were still ashore.
With the facts at hand, this sounds like a huge "oops" for RSSC.
Dena