It's simple, kismet and airodump-ng for that matter are sniffing the air for a prolonged period of time so have many chances to capture the beacon. Wireless assistant is only sniffing the air for a few moments at a time, when you tell it to refresh. If the AP has not sent a beacon within that short period of time then it will not show up.
By the way, wireless assistant sucks, stop using it.
The card has nothing to do with it in this case.