I am also having the same problem , i have a logitech dual action controller and it isn't recognizing it, hence the grey out , i bought the retail version, aka, dvd, so don't know if this applies here or not..

On a 360 controller they seem to have changed a few things... left-analog doesn't scroll through quick-menu anymore, but dpad works fine, and same for in inventory/craft screens... analog not working, dpad works fine.

Also, although the patch reset my User.ini changes in Documents folder, I was able to change the Back button to be the Medallion again.

Most annoying/frustrating thing about this is that the right analog stick (thumbstick) does not work for text scrolling in journal anymore (mouse scroll wheel works as an alternative until they fix this)... but at least they fixed character attributes screen problem (oh the irony fix one thing and break other things). :S