if you are fitting your new stereo in a mk 2 take out the stereo and check the wires on the bottom connector.
i too had this problem and it turned out to be that.
on your connector you have,
top block is power and so on
second block is for your speakers
and the bottom thin block is for your swc.
check these wires, on mine two of them where in the wrong place.
just remembered i bookmarked the page,
give this a read it tells you in better detail, hope it helps.
if not worth a try.
EDIT. just checked and the image has been removed but you will be able to follow the direction given.