I found a recipe for Cookies and Cream Brownies. First time I made them they were great, in a 9x13 aluminum pan. Second time, I used an aluminum foil-type pan that you take to potlucks, and while the cheesecake was completely baked on the top, there was raw brownie batter on the bottom, giving the appearance of a fudge sauce on the bottom. It was really weird, that it didn't even partially bake. Does this happen when using the foil-type pans? That's all I can think of. The directions do not say to bake the brownie first then put the cheesecake on top and bake more...you bake at one time.
One thing that can matter is that darker pans often absorb more heat (from radiative heating). So if your 9x13 pan is dark-bottomed (e.g., nonstick, or darkened from years of use) it'll run hotter than a shiny foil pan. I'd be surprised for that to result in raw, though, normally its just more or less browning.
If you put a baking sheet under the foil pan, that could also function as an insulator, especially if its a steel pan instead of aluminum.
I'd guess instead some other "human error" thing happened: measured and ingredient incorrectly, left something out, added something twice, set the oven temperature (or mode!) wrong, etc.
It sounds like you've already narrowed it down. The foil pan does not conduct heat as well as the aluminum pan, which is causing the bottom to go uncooked.