+1 on the connector.
Replace the jack, check and re-soldier all connections, pull the wires out of the speaker connectors, clean the wire and put it back in.
If the amp has not...dare I say it...been recapped, consider have them replaced. Definetly look over the head and make sure everything is still soldiered and tight. Clean the jacks on it as well. Check the tubes as well.
Line the cabinets and amps up with long speaker cords and try the swap again using one amp on each speaker, then changing to the next speaker. After trying the first amp, change to the second and fdo it all again. Play the same instrument with the same cords. Keep notes of your findings. Many times swapping stuff around and not tracking the changes can lead to errors in what you think happened. Personal experiance speaking...after hours and hours of searching...turned out to be a bad cord.