You should only pay for new ratings to be added to your licence.
If you already hold a PPL with a valid SEP rating then it should carry across to your CPL. It will appear in the "ratings to be revalidated" section but you'll have to transfer the certificate of revalidation page from your old licence to your new one.
However, if you've never held a SEP rating before (i.e. you're an integrated course graduate) then you have no rating to carry across and you'll have to pay another issue fee. This is a pain, but since you've already paid for the flying to be entitled to the rating I can't see why you wouldn't want to claim it!
Hope that helps!
Al
[Edited to point out that you should always double check these things with the CAA if unsure - Al]
Last edited by ATP_Al; 22nd Jun 2005 at 13:58.