it isnt a problem, when updating from a b unit, it changes it to a D.
i did MK6Greg's update last night and his changed too.
Just load the maps and you will be ok.
Sometimes if using a modified firmware to prevent battery drain issues, there are some things that take longer to start up. Its nothing you should be worried about.
If its something thats really bugging you, then update the canbus and install a higher firmware like 4120,