I'm having the same issue. All renpy games preferences, gallery and seen text history are not saving. I change music volume, text speed, etc. but after i relaunch games all values return to default. I'm using win 10 pro on vmware workstation pro and all applications work without any problems except for renpy games. Some games still work normally like Pale Carnations, but most don't for ex. Power Vacuum.
EDIT: it seems that games, which have "sync" folder in their appdata renpy save folder, are the ones with this problem. Still don't know how to solve it.