No, there's nothing wrong with the OP arriving twelve hours after the official check-in time for his resorts starts, as long as the arrival is prior to the accounting system's 5:30 AM or so next-day rollover. THAT'S the start of a whole new hotel/accounting day and could invalidate any reservation made for the previous day. MANY people who drive to Walt Disney World arrive in the middle of the night.
Expecting to make a reservation for, say, a Wednesday and be able to check in for that reservation on a Friday would be disingenuous. ANY hotel would be entirely within its rights to have cancelled that reservation at least eighteen hours earlier, leaving the guest with no place to stay - yes, even with a fully paid reservation.
Respectfully to the OP, the response from the Disney Cast Members may have been a reflection of your attitude during the call. I'm not saying it was - I don't work for WDW, I don't have the slightest idea who you are, I have no idea how the call went. Your tone may have set the tone. It's possible your family member was just nicer during the entire call, so had a better experience. Maybe you just have a gruff voice and sound aggressive or demanding, and your family member sounds friendly and jovial. That shouldn't affect the response you each got - but Cast Members are human.