Controller buttons performing extra actions

Ourorboros

I've been using a controller with Xpadder since early release. Outside the limitations of this combo, it's served me well. I played all week without enabling Gamepad mode. I finally enabled it last night to see how it works, and ran into a problem I cannot clear.
When trying to interact, as in mining or collecting wood, the Y button is being triggered, firing off that slotted ability when I press A. When I roll dodge using LT+A, RB is also triggering. There are a few other similar confused buttons. I have been through the key bindings looking for any overlaps or conflicts, and set both keyboard and gamepad settings to default. I'd like to keep the gamepad mode, as it works much better for me on a 55" screen....the increased font size are a god-send to my eyes. But the issue I'm having is a game breaker. Is there a file or setting that can correct this?

edit: Even though I was careful to make sure Xpadder was not running, it feels like there is a conflict between some of the gamepad controls and those I used with Xpadder.
[Wipes egg from face] I found the solution, in case anyone else is as dumb as me. I was sure there was a conflict with my old Xpadder settings. I was sure Xpadder was not running, and there are no references to Xpadder in user.settings.txt. Turns out, Xpadder was still running in the Tray. Once I closed that, all was good.