Teri, I have this same problem with 3 of our 4 AP's. One AP number does work on the website though.
I think I know why those 3 don't work. I carried all the AP's for my family and never realized that there was a weak magnet in the snap of my purse. The magnet erased 3 of the AP's and they had to be replaced at guest services when they couldn't be read at the gates. The WDW passholder webiste does not recognize the numbers on those 3 replaced passes but does accept the number on the one AP that wasn't replaced. I'm just wondering if the new numbers weren't entered into some master system to make the replaced passes recognized on the website. The replacement passes work fine at the gate entrances though.