You shouldn't modify your game installation.
When you've uninstalled the game, it didn't remove the backup folder (because for the SEGA uninstaller it never existed). Then you re-installed the game in JP to the same location, where there's already a backup folder, which prevent you to install the patch. Simply delete it manually. Then re-apply the patch (it's ok if you keep the language in AE at this point), and see the problem reappear. It's probably because you're using an anti-virus which detects the crack as a virus, and block its execution. It's a false positive. Try to disable it (or place PSU in its exclusion list).