I confirm that those issues are produced by the fact Memoria now uses a custom save file on top of the normal save file: there is no problem in reading datas for the save editor but the update of the datas is done only in the normal save file and not in the custom one. That is why the changes are not taken into account in-game.
As faospark showed, the normal save file "SavedData_ww.dat" is still there (it contains all the normal save slots), and additionally there is one custom save file for each save slot (+ the auto-save). This custom save file is similar to the normal save file but doesn't contain all the datas (for example it contains a registry "40000_Common" but it doesn't contain "30000_MiniGame", at least not yet). There also are a couple of differences for taking care of the features added by Memoria.
As always, the source file
JsonParser defines the save file format. I'm here in any case to answer questions if you need, gjoerulv.