have you solved your problem with JoomFish + MosetsTree?
"After weeks of deep testing we have noticed that evertime you edit a listing using mtree backend, the value of each custom field id in the jos_mt_cfvalues increases by one, thus breaking its reference with the jos_jf_content reference_id field which remains unchanged. that's probably why joomfish is no more able to find the value and picks the original one provided by mtree."
