Even though I often encountered this problem too, but I'm not sure if this is a good idea. Actually when the chat box disappeared, you can simply press Enter again and the text you already typed before will appear again.
I think the reason they made the chat box to disappear when the mouse cursor hovering the joint is to preventing you to accidentally typing Z, X, C or V because from what I know most people playing using that keys to control the joints faster rather than just using mouse(including me).