OK, so I installed 4.4.2, went thru the JB process (tethered is a PITA in general, but it worked first time, so… not really worried!), and then restored my settings.
Yup, looked like nothing was restored. So I used Mainenance -> restart ATV (ie, restart the software, not the device), and low and behold, all my stuff is there - Media Center, mostly, including MC passwords to get to my Drobo. Which is FANTASTIC.
Maybe, after a restore, offer to restart, the same as if you updated maintenance/mediaplayer etc??