Axial Flo
I haven't received my pack yet, but my guess is that the Personal Benefit Statement is calculated for your situation today (or at 6 Apr 06), with the calculator then being available for you to explore various future profiles. After all, the "system" cannot know for sure when you will finally retire. The calculation may not even have been done at this year's pay rates, and will have been produced a little while ago.
At least, that's the only way I can make sense of what you describe.
D4RP
The "Specialist Aircrew" daily supplement in the PAS Pay tables is only for the Army, who have certain types of people they refer to as Spec Aircrew. It is not Spec Aircrew as the RAF knows it, since it is nonsensical to have RAF Spec Aircrew on PAS terms. This might be the source of the confusion (its not something I have come across). Double check that you are making all the correct Service, Rank and Unique Pay Table selections. Come back if you can't sort it out and I'll take a look.
Regards
Ginseng