Whenever I start up free play now, tori and uke are always above the ground, standing beside each other. It's in every mod. How do I fix it?

Well my first thing I'd do is re-download Toribash client.

I don't know why this is happening to you though it's never happend to me so I can't give much advice other than re-installing toribash

probably best wait until you hear from others.

Write /set engageplayerpos 0 and it will be fixed.

You're god.