After Playing In An Old Version Auto Jump Always Gets Activated

Are you running it in the same installation?

The controls reset because the key binding parameters are way different between versions and each version treats the other's settings as incompatible, setting them to default. The best thing you can do is using launcher profiles with separate directories for alternate versions, therefore, each instance will have its own options.txt and won't conflict.

Downgrading is not, was never and will never be officially supported. Please keep your different versions in separate folders using the launcher's launch folder feature.