I am having the same issue: links to youtube videos are not showing up as embedded videos, they only show as the link.
I am using ACF 4.1.8.1 and WP 3.5.2. I’m showing the content by applying the the_content filter on the get_field.
It’s strange, some videos are showing up, but if I go in and resave the post, then the videos do not show up anymore.