I had a late night arrival in December with my daughter. We were originally scheduled to arrive at 11:00 pm, but with a weather-related delay - we didn't get there until 11:50 pm!
We had used the yellow tags on our luggage, so we just walked off the plane with our jammies in a carryon, hopped right on the waiting monorail to the terminal, and were at the Magical Express Desk by 12 am on the dot!
I checked in, and gave my luggage claim numbers to the clerk at the desk, and he directed me to the queue area, where we were the only ones in line, I was met immediately by another CM, who double checked that I was going to Pop Century - she then radioed a bus driver, and said - "I have a party of two going to Pop Century, can you drop them there on your way?" We were then escorted onto a bus with about 10 people in it (not sure where they were going). My daughter was REALLY happy to see they were playing Lion King II on the DVD player. Less than 5 minutes later, we were rolling down the road!
Pop Century was the next stop - and we were there before 1 am! Obviously - there was no line at check in , since we were the only ones getting off the bus. Just an FYI - the computers go down for maintenance at 12 am, so you'll have to come back in the morning to add your credit card for charging, etc.
We were asleep by 1:30 am, and I didn't notice the message light blinking till I came out of the shower at 8 am. The message time said 6:15 am, so they must have just lit the light without ringing it through (I am a light sleeper, and would NEVER sleep through a ringing phone.) The message said that they had my luggage, and would send it over as soon as I called. I called at that point, and my luggage (at Pop Century - without a big valet staff!) arrived at my door in less than 10 minutes.
I cannot fault any part of Disney's ME service that night - I too was worried with that late night arrival - but it worked beautifully for us - and it was free!