Hmm not sure whats wrong then, i currently have a multisite setup with custom fields working on WP 3.9 so it is definitely still compatible.
Although i have mine in a plugin instead of my functions.php file, you could try that ?
Cheers
-Harry
Hi Physalis,
Just to rule it out in case, do you have ACF activated network wide or just on the main blog ?
Cheers
-Harry
Just to add to this.
5) Go back and trash the fields from the main site so there aren’t duplicates.
I found instead of deleting the original fields i just put the outputted php in this if statement:
global $blog_id;
if ($blog_id != 1) {
//Output here.
}