Ok so I solved it.
I just ended up downloading Launch Box again and moved the Big Box app shortcut to the current folder.
I found out why that auto scroll was happening. Apparently my Xbox One controller's Left Button was stuck pressed down. I found this out by starting up a game(SMB 64 DS) just using Launch Box instead of Big Box and when I was running outside the castle yard, every time I would try to turn left or right using the analog stick, it would try and turn the camera. In SMB 64 DS, holding down L and pressing left or right turns the camera. So I was like, "Great, now something changed all my bindings". I then immediately tried pressing down on the LB and realized, "oh shoot, its stuck". After getting unstuck, it solved that camera problem and I thought, "...wait a sec, maybe this is causing that issue with Big Box". Guess what? It was. Big Box works great and now I'm happy.