I've seen this happen when the wires going to the economizer plug were squished between the blower housing and the top of the unit, rubbing through the common 24v wire. That'll make all the contactors chatter. That doesn't really explain "the bypass plug fixes it" though.
Been behind a many a tech who missed this. I've seen many of these with a short in 24v red leaving lvtb going to economizer, sometimes in blower compartment, sometimes just in side filter section where wire passes thru. Also, does it have the high static motor with internal overload? Seen that cause intermittent problem too