Assuming you're using an Internet speed test, there are too many factors involved to consider it a valid test of wifi throughput. You'd be better served looking at client metrics like RSSI, Tx rate, or SNR.
Having said that, perhaps there is considerable contention on a particular channel as a result of co-channel interference or interference from other electronic devices, like microwaves, etc. These particularly affect 2.4 GHz connections. You may also want to look at the layer two connectivity between the questionable AP and its upstream switch, e.g. duplex mismatches, CRCs or other errors.
