I just checked the results from the 2001 MTT to Chamrousse, and the rules were the same back then. Ullrich 2nd in the stage after Armstrong, but only 3rd for the points on offer on Chamrousse.
Previous case in the Tour must be from 1997, right? Does anyone have the intermediate times from back then?
A more recent example would be the TT in the 2013 Tour which had two cat 2 climbs in it. The second checkpoint was at the top of the second. Contador was fastest through, but didn't get any points as others went faster up the climb.
Also stage 1 of the Giro last year. Ciccone was basically the slowest to the bottom of the final climb, but then did it quicker than anyone to claim the points.