Bug/Issue PS4 Controller and In-game Lobby bug.

Greetings. My friend is having a problem with her ps4 controller. We tried looking all over the net for solutions, but apparently its a new issue. We did look around the steam's big picture, but it didn't help either. Her controller works fine on other games (Overcooked! 2), but when she play Stardew Valley, the buttons somewhat switched automatically.

We read the default mapping that on Dual shock 4 square is supposed to be action (Swinging axe, casting lure for fishing, etc), it somehow switched to circle instead and now square is not assigned to anything. Triangle was supposed to show the crafting menu, however its popping up the world map instead. The select button is switched to action too (Swinging axe, casting lure for fishing, etc). I tried my best to reproduce this bug, but I couldn't on my side.

I'm thinking that maybe a file in the folder messed up her control scheme. Is there a specific file I should look into?

Also, the in game lobby is showing multiple times. Whenever a person joins it, they have to create their character for each. I have attached a screenshot of the multiple lobbies.

Thank you, hope to receive some help soon.

Edit: This happened on Windows. (I'm using Win7 and she's on Win10)