Oops, guess I misunderstood which patcher you were talking about. You'll know that ragnarok_re.exe is finished patching when it brings up a dialog box saying something like "20% ?? ?? ??," with "Yes/No" options. Click "No," and it'll apply the patches. You can always run it a second time to check that the patches actually got applied, if it doesn't download anything, you can just hit Esc to close.