I have a Kef 3005 system and it all works fine when playing blu-ray etc, however when I play a CD and select the BD input there is activity coming from sub.
You will probably get a lot less bass from a CD as there is no 0.1 track on it, so maybe there isn't quite enough to kick the sub into action on the auto setting. Is there a permanently on setting on the sub you could try to check this?
What 'Listening Mode' are you using? Settings like 'Direct' don't use the sub, 'Stereo' on the other hand will utilise the subwoofer (depending on your gear of course).