It probably relates to the tuning you're used to. Piano strings do not have perfectly linear overtones, and thus piano tuning is never 100% equitemperal (I've tried; it sounds quite off). So the tuner has to make concessions across the scale, and most likely, there are more of them in the black keys since they are typically used less and you'd typically start with the pure intervals from A anyway.

Of course, since you hear this effect even when played one by one, this assumes you are unconciously comparing them to some reference pitch. (I'm not aware of anything in manifacturing of piano strings that would somehow make black strings be produced different, so unless I'm missing something, it would have to either be in terms of key mechanics, hammer wear, or tuning.)