I just went over to my setup with my Republic Gunship (to attach the turret pod), it's pretty much my only purely Ep 2 setup. I get in there, and first I notice that my POTJ preview Clone Trooper's feet has completely stuck to the floor and footpegs he's on. As I'm working this out, I look over and see Saga Arena Escape Padme and her torso is FULLY yellowed, horribly so in fact. Then I look behind her and the Clone Wars realistic line Clone Trooper's torso is also yellow!
I have a couple more of those Clones handy, and 1 of them has also got his torso yellowing, while the 3rd barely has it starting. Due to the fact that the less yellow clones aren't in the Gunship, I can only conclude that the gunship itself is what's turning them yellow. Maybe it's a coincidence, but it's not the sun because there's another clone in there facing the lighter side of the room who doesn't have yellowing, and the yellow figures have it evenly.
I guess this was bound to happen. I wonder if in another 5 years we'll be noticing the same problem with Ep 3 and The Clone Wars figures as well.