This is been bugging me all day! So i went through ever single race again a and b spec to check if i missed something and i havnt missed a single race or championship, everything golded no 4th place or below in anything. Same in licences all completed to bronze and above.
Did you check to see if you received the prize cars for the Championship wins?
A-spec Championships:
--------------------------
World Compact Championship----Hommell Berlinette R/S Coupe
Clubman Cup-------------------Honda Mugen Motul Civic Si Race
Gran Turismo World Champ------Bugatti Veyron 16.4 '09
Tuned Car Championship--------HPA Motorsport Stage II R32
Japanese Championship---------Gran Turismo 350Z RS
GT All Stars--------------------Amuse Carbon R R34
Polyphony Digital Cup-----------Nissan 350Z Gran Turismo 4 Ltd
NASCAR------------------------Pontiac Tempest LeMans GTO
Formula GT World---------------Caterham Fireblade
Dream Car Championship--------Ford GT LM Race Car Spec II
B-spec Championships:
-----------------------
World Compact Championship-----Autobiachi A112 Abarth '79
Clubman Cup Championship-------Toyota Celica TRD Sports M ZZT231
GT World Championship-----------Pagani Zonda R '09
Tuned Car Championship----------Honda AEM S2000
Japanese Championship-----------Opera Performance 350Z '04
GT All Stars----------------------NISMO 380RS Super Leggera
Polyphony Digital Cup-------------Gran Turismo Skyline GTR '01
NASCAR--------------------------Mercury Cougar XR-7 '67
Formula GT-----------------------Suzuki GSX-R/4 Concept
Dream Car Championship----------GT by Citroen Race Car
Checking for the prize cars wouldn't be conclusive since you can win the prize cars without finishing first in every race. You can win the prize car even if you haven't won every race in a Championship Series, if you have the most points at the end of the Championship.
I actually tested this last night as well. I won the prize car even though I came in second in every race in a Championship. I engineered the finishing order by some judicious blocking so that a different car won each race and I always came in second. This gave me enought points to win the Championship, so the game awarded me the prize car. After the races the game shows that I have three silver trophy's and the Championship trophy.

I'm not sure what else to suggest....... You could always start a new game!
Good luck!
GTsail