This is an issue with WP1.6, I think.
I ran into the same problem when writing a custom import script. It seems when running wp_set_post_terms you must use term names (slugs) rather than IDs.
Only the categories taxonomy uses IDs, now.
Ref: http://codex.wordpress.org/Function_Reference/wp_set_post_terms
It seems the ACF plugin is setting the terms using the term IDs, rather than the slug. If that’s the case, should be a simple fix. 🙂
