I'm not even in the beta, it was the recent official release update that happened a week ago or so. I think the issue may have been more with Steam than the controller, so maybe a client update was what fixed it.
The same employee in question basically said that it is indeed with the client itself. Maybe they did a revert on the normal client or something?
On the beta client I'm still losing configs if I back out before exporting, but the whole thing is a bit snappier now.
EDIT: Nevermind, spoke too soon. Gaaah. ><;
EDIT 2: This part is what really makes you believe in the Steam Controller.
Not the best score around, but the mere fact that I can go into a casual game of Counter-Strike and keep a positive score using entirely the Steam Controller is just awesome.