No reason - it should be accepted. As well as "I had been waiting for you" and simply "I waited for you". Report it.
Russian has only only one past tense, so it makes no distinction between these English tenses. A context takes care of the precise meaning.
Furthermore, even if you decided to go for genitive (which you should not in this example, but that's the other case possible with "ждать"), you'll get the same sentence as the genitive and accusative forms of Вы coincide.