It's funny that this would be posted just after I joined, because it's something I've been wondering for at least a decade. More than once I've shouted at the TV: "BUT DESIRE IS
I've always held the personal opinion that Data does have emotions without the chip, but that they're very different from the emotions of a human and he doesn't recognize what they are. Recognition of this at some point in the series or movies would've been extremely awesome, and I do think it's a real shame that there wasn't more emphasis placed on Data's successes in his quest for humanity.
I can't enlighten you as to why this apparent contradiction was overlooked in the show, though. The writers didn't realize it was a contradiction, maybe? I honestly don't know. The TV never answers the questions I shout at it.