Stops working once Pokemon SwSh starts

I've followed the guide to a T, but when I start Pokemon SwSh, the bot no longer controls the Switch. If I run the bot in the Switch main menu, it controls the Switch just fine. This is really frustrating and I've been googling all day but I can't find anyone else with this issue.

If I can't have the game controlled by the bot, then there's no way to make this work what so ever. I've been using Atmosphere as my CFW, do I need to be using a different one?

Has any one out there experienced this? It completely defeats the purpose of the bot.