I'm also having new mouse issues after today's patch, but they seem slightly different than yours. I often switch between mouse-cursor and freelook mode; prior to today, this worked fine, and when in freelook mode the mouse cursor disappeared (as it should) and the cursor position was clearly locked in place (as it should be).
Now, however, if I turn very much in freelook mode, the mouse cursor suddenly appears and moves outside the game window (generally to my second monitor), which messes everything up in game. I never had this problem before today.
Did something in today's patch change the way mouse positioning is handled when in freelook mode?