I think Tony Stark might not be in the Iron Man suit, and he’s multitasking while doing something else. Otherwise, I don’t see how Frank Castle, even with a War Machine armor, could beat him like this. Also, wouldn’t the first thing Iron Man will try in this scenario is to hack or shut down the War Machine armor, he built it after all.
From – The Punisher Vol. 1 #228
Nick Fury Sr. must have made sure even Tony couldn’t access the armor. As some foes have given him some difficulty by making it so Stark can’t get through. That or as you said, he is remote piloting the armor.