Melta damage drops off with distance - you can see how much by holding ALT while aiming with it. I'm guessing you weren't close enough to melt the armor.
I was right next to the wagon, it's the only safe place: you shoot, then you get in and it can't kill you. That is why I'm pretty sure my shots were accurate and had the maximum power. I only could destroy both turrets after having spent six hours on it, it took me thirty five crak grenades and in the end, when I tried to shoot it with a rocket louncher, my space marine didn't have enough time points to get in, so the cannon turret tried to kill him, but as he was standing right next to it, it destroyed itself instead.
Really, those ork wagons can't be that tough! I don't know a lot about the 40k lore, but I thought melta takes down wateaver it is used against, except spaceships, probably. Ten melta shots, several crack rokets and a bucketful of crack grenades is way too much.