There are too many things that could be causing the values not to be saved correctly.
1) acf_form() event when used in the admin, requires that acf_form_head() is called.
2) values submitted using acf_form() are usually processed differently then how acf normally does this for admin submission.
3) unknowns
Why not use acf to hide the “feature image” meta box and create your own using an ACF field group?
