For the longest time, this issue has plagued me because I hadn't sat down and tried to fix it and looked stuff up properly lol. I was doing most of my development and testing with keyboard, but enough people complained so I tried to fix it once and for all!!!
As a result, I have done some changes to the configuration. If some of your controller mappings got messed up, I am sorry!!! It's for the greater good!! Maybe.
Let me know if things are still weird.