Nintendo Switch Pro Controller acts as a mouse instead of a gamepad on PC?

Sounds like you have Steam configured with a Desktop Configuration that binds the joystick to mouse movement. Connect your Switch Pro controller and open Steam, then go to Steam menu -> Settings, click "Controller", and click "Desktop Configuration". This should launch Steam Controller Configurator with the Desktop Configuration profile.

To unbind the joystick, find the rectangular region that shows a line pointing to the joystick when you hover over it. Click the region, a dialog should pop up. For "Style of Input", change it to "None". Click Back to close the dialog and then Done to exit the configurator tool.

I had a similar problem with my Xbox360 controller. The way I have solved it now is to disable Xbox configuration support. To be honest, I'm not yet sure what the side effects are, but at least for the games I play, it works.

Open Steam, go into the Steam menu > settings > controller > general controller settings. And in your case, uncheck Switch pro config support.

For reference, this is where I found the solution: https://steamcommunity.com/app/353380/discussions/0/133256959376939467/