(1) Are you baking them upper/lower or side-by-side?, (2) Is your oven's outside width 24" or 30"?, & (3) Gas or electric?
My guess would be that either you have a 24" oven and you're baking upper/lower or you have a 30" oven and you're baking side-by-side. Either way, I think the ultimate culprit is heat circulation - certainly you wouldn't be having this problem in a convection oven, right?
If you're baking them upper/lower in a small oven, I believe that heat absorption would probably create areas of lower temperature above both pans that wouldn't even out well without convection. If you're baking side-by-side in a larger oven, I believe that the total area of your pans would create a heat block and a temperature differential between the top and bottom of your oven that would not dissipate well without convection. And while I think the circulation problem would be less of a problem with gas, I'm pretty sure it's going to present a problem in either type of oven you use.
Being the owner of a 24" electric oven myself (so the interior of my oven is 18" x 18", not including the ribs that support the racks), I can't even bake two 9" circular cake layers at the same time (either diagonally or upper and lower) without grotesque deformations in the tops of my cakes. And two 9" round pans with a thin layer of cake batter are going to be less of a heat magnet and obstruction than a thick layer of apple cake batter in two 9" x 13" pans.
Ultimately I think the problem is not one of time but of maintaining temperatures above and below your pans - and adding time to the bake won't resolve the problems caused by such a differential. Alas, I believe that your best option is to give each cake its own space and time in the oven. Whether it's a heat conduction issue or a circulation issue or some combination of both, I think the variables involved are WAY too complicated to ever lead to a general baking time extension guideline when doubling-up a recipe.
Bake them separately - and, yes, I realize that's not a very satisfying recommendation.