I assume that you had just updated your Marketing Channel Processing Rule to use the Query String Parameter as the channel's value. So before that, the channel's value was the referring URL.
AA does not change old values, it will just start using your changed setting for new hits. So when you run a report, you should be running it for a date range that starts from after you had changed your Marketing Channel Processing Rule. If your report's date range includes dates from before the Processing Rule change, then you should expect to see the old channel values, i.e. the referring URLs.