I suspect this has something to do with the install for All Users / Just Myself option.
The installer used to say it was installing just for the current user, but was really doing All Users. I found the installer script was using the values backwards. Perhaps this is the cause of the new problems. In the past, they'd installed by default for All Users, thinking it was just for them, but now they really install just for them and so Replicator is looking into the wrong AppData folder?