I think 2K3 follows the same layout as XP - A B C D where A and C are exactly the same.
VX, Ace and MV follow an A B C back and forth pattern, where B is repeated (A B C B A B C B ...)
So to convert a 2K3 animated autotile to VX/Ace/MV format, apart from resizing, you would take the 4th, 1st and 2nd blocks and paste in that order into the new tilesheet.
2K3: A B C D
MV: D A B