I wouldn't care much about IS rejections. I once had a rejection, where the inspector criticized something in the animation which wasn't there. I had some Sun animations with flares and some without and he even criticized the flares in the clips without them. In this case I complained and got right, but usually I don't reup to IS, it's not worth the time, if other agencies accepted the clip.
Maybe in your case the inspector just used a wrong player.
I upload my animations always as .mov photoJPG and never had problems.