also ran into this issue today. Whats the solution? Just wait until things become fixed?
Well, I know this is HTC section but It think this does not matter....
(Nexus-S, CM7, matr1x kernel)
i forget what i did exactly, but try replacing 'su' and 'superuser.apk' with a newer one..., make sure your updater/update-script is installing su properly
same thing happened to me. I got a notification saying su binary outdated click here to update. I clicked it and it failed to connect. so I just kept clicking retry again and again it worked after about 5 tries.