You, found the issue, it was with the Build itself. You hadn't decrypted the Main Build files yet (the "Game.rgss3a" file). My bad, since I usually deal with the Decrypted build, I got too used to it and forgot Bo Wei distributes his game in encrypted form. The decrypter program is public on the internet (quite a few of them for this), but I decided to make it easier, and added a light (on memory size) decrypter to the Merger Files, along with instructions on how to use it.
Check the mega link for the Merger Files, there's a new version now there, also explaining how to use the Decrypter. Afterwards, everything else should work for your Saves, I checked them with a properly-merged build. (simply exit F6 South and try to re-enter).
It didn't work with the encrypted files since the game (all rpg maker games) always defaults first to reading the Encrypted file, ignoring all decrypted files (and the SCp3 and Merger files are decrypted files). If you delete de Encrypted file after decryption, then it will read the decrypted files instead.
Thanks a lot for finding this, since not everyone knows about the Decryption stuff, and now I was able to add this step to the Merger!