It was a brand new game. I didn't look at the console. I did try to use cheats at one point, but the battle skip option seemed to completely break the mod so I started a new game without it. Unfortunately I don't have that save anymore as I just restored the original game files, which restored the button to get past it.
Edit: Happened again with the Princess' Braclet subquest. Button wouldn't show up when the mod was installed.