Are you using the same speaker cable on both cabinets?
Or does the "good" cabinet have a different cable? I've seen instances where a dodgy speaker cable caused weird things like this. Also, something wrong with the jacks on the speaker cabinet could cause this odd sound, too. I've certainly seen abused/dodgy NL2/NL4 jacks before, especially if moisture somehow got in them. They are self-cleaning to a degree - so twisting them on and off can usually brush off any crud, but sometimes it doesn't.
Or does the "good" cabinet have a different cable? I've seen instances where a dodgy speaker cable caused weird things like this. Also, something wrong with the jacks on the speaker cabinet could cause this odd sound, too. I've certainly seen abused/dodgy NL2/NL4 jacks before, especially if moisture somehow got in them. They are self-cleaning to a degree - so twisting them on and off can usually brush off any crud, but sometimes it doesn't.
Had the amp on for a few hours now and it sounds great as ever.