I haven't seen any problems with this anywhere else so I don't know what's up.
Basically, I have added a PNG sequence and animated it onto both the Background Layer and the Floor. The background is as it should be, however the floor is darker when I render it out. I don't think it's a matter of lighting since I've done this sort of thing many times without lighting and it's worked just fine.
Also, when my friend creates the same thing with a floor and a background and I load it on my computer it works just fine, making me think it's not something wrong with the installation and whatnot.