This is a ‘save order’ issue with WPecommerce (getshoppped, wp e-commerce, etc for anyone looking for those tags). Both ACF and WPEC user ‘save_post’ with a priority of 10.
By changing WPEC save priority to an integer lower than 10 seems to have solved the issue – no more serializing the data as WPEC custom field and thus overwriting the ACF data.
!IMPORTANT – THE FOLLOWING FIX WILL BE OVERWRITTEN WHEN YOU UPDATE WPEC!
This fix is for WPEC version 3.8.10. Visit product-functions.php (\wp-content\plugins\wp-e-commerce\wpsc-admin\includes\product-functions.php) on or near line 221 is the following code:
add_action( ‘save_post’, ‘wpsc_admin_submit_product’, 10, 2 );
Simply change the save post priority from 10 to 1 and the issue should resolve.
Remember, this is NOT an issue with ACF, this is a race/save conflict occurring between two augmentations of the POST that are trying to submit on top of each other.