I had the same exact issue and it was coming from a select2 JS conflict between “ACF Pro” and “Paid Memberships Pro” plugins. Once I used wp_deregister_script on the PMPro enqueue of select2, ACF started to save again as a serialized array. The weird part is it used to work ok until the last ACF update (PRO v5.5.10).
I know it is not a good solution to deregister JS/CSS of another plugin so there is probably a better solution to fix the conflict.
I Hope it could help anyone with the same issue.
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