Nick,
After tearing my hair out over this controller, I am now convinced there is something wrong with the Asio Driver compatibility with my PC, you are not running Windows 10 by any chance?
After a Million Technicians telling me to, change this!! - swap that!!, I know it is not my PC (as I have 3) also my DDJ-SX2 and DDJ-RR run perfectly with no issues at all.
After I installed the new updated Asio Driver 1.11 my DDJ-SR Controller started acting strange, First of all I would have no Sound, then after I had managed to fix that, when turning on the Controller one day, I had some lights missing (both right hand pad lights, right deck Load light, both Sync lights, etc) I am convinced the Asio Drivers are messing with my controller hardware, if you run a rival Dj Controller software company you can get around this, but not with Rekordbox Dj or Serato.....