From experience with a previous car with light coloured carpets (not a Jaguar though) it's quite likely that although not obviously dirty, your original carpets have accumulated quite a bit of dust and general grime over the years which make them look darker. The new mats are probably what the carpets looked like when the car was new. Some part of the car, particularly near the vents in the rear parcel shelf, gather more than others but it's worth trying a carpet cleaner on a small patch to see what comes out.