As of 1.5.2, I notice that animated textures on new objects will now put the texture upsidedown on one side using llSetTextureAnim.
You start with a prim with texture on one side and another opposite it. Same texture both turned rightside up. For some reason as soon as it starts animating, one side of the prim is fine, the other side immediately gets turned upside down and nothing you do will allow it to be turned around. The "flip" checkboxes don't make a difference.