Overtones
It could be a speaker,but usually that sounds like a rattle or vibration.4-12 bottoms are quite often heavy with
undesirable low overtones.....does it sound this way in the room,or just on playback of recording?Have you tried an EQ in your rig to filter out the nasty tone?A parametric would help.If you are only hearing this sound on playback,try different mic positions,or a different mic.Even though we all love the sound of a mic'ed amp over "direct inject",it is pleasing at times to mix the two,if tracks allow..blending a tap of the amp's preamp out with the mic.
I don't know if this has been any help.....I don't know what else to offer,outside of testing each speaker seperately,or checking the impedence of the cab. Good luck!