This APD a normal customs charge at Heathrow (and I assume any other UK airport) for any type of ticket. Doesn't have anything to do with the GPU waitlist.
http://customs.hmrc.gov.uk/channelsP...document#P1_33
All my pmUA LHR trips have this government charge on them. I honestly think you might be overlooking something from your past trips....maybe it was hidden in a broader fee category or something.