I just watched Skyfall and immediately noticed a small, gray rectangle on the bottom of the screen where subtitles would normally go - very annoying.
After reading this thread I stopped the movie and changed the subtitles setting from "Off" to "English" and can confirm this removed the gray rectangle.
I also purchased Argo a while back and experienced the same issues others mentioned where subtitles would stay on screen until the next one came up. Have just re-checked using subtitles set to "English" and can confirm that this no longer happens - haven't watched till the end to see if the last one stays on though.
We also own an Apple TV 3 (a recent purchase) but it's not practical for use with iTunes movies because of painful buffering issues - as noted in threads elsewhere. Also, when you purchase a movie, it doesn't sync back to your iTunes computer - fine if you live in a country with fast, all-you-can-eat internet, but painful if your internet is calculated based on traffic usage.
We'll be sticking with our Apple TV v1 for as long as possible so hope this subtitles issue doesn't come up again.