Why are my woofers pumping?

IMHO, you need a filter, or (cough), an eq to filter out anything below 15 hz. Some of it could be acoustical feedback.  I thinks it’s much more simple, than a mismatch or incorrect setup of tone arm/equipment.

O_holter:  I'm convinced your problem comes from acoustical feedback. With a TT, placement is vital. I too had the same problem.  After months of experimenting, I found that TT platform isolation cured my problem. I built a suspended platform using heavy duty dampened springs and cables. (my room is on a suspended floor on the upstairs portion of my house that exasperates the problem)  I also noticed feedback on my Theta Miles CD player, when playing anything with a lot of elf and high db levels. I installed four steel cones on the bottom of the player and now I enjoy outputs of 90 db+, without any adverse effects on both playback systems. Most rooms have areas, where the low frequency is somewhat exaggerated. Be sure your TT, as well as your CD transport is not in one of these locations. 

If you’re hearing a periodic bump and it’s keeps a perfect rhythm, has to be in your transport, except you said it does it on cd too. 🦄

O_holter. As I said and agree with CT_0517-I think it acoustical feedback going back into your cartridge. Today I am trying some new phono interconnects and they’re shorter, so I had to take one TT off my “floating” support platform and placed it beside the speaker.  My TT platform is on my left side wall.  Anyway put on Supertramp Crime Of The Century, which is not that bass heavy. No main speaker woofer pumping, but my two JL-Fathom 113’s didn’t like it at all. I was convinced your problem was acoustical, but I read you experienced almost the same problem with cd’s and that it had a rhythm to it like going over a road with expanders in it. Bump...bump... bump...etc. If this is what you’re experiencing, it has to be TT related-except you said you heard it when playing a cd too. My advice-hire an exorcist. Can’t see anyway you can have the sound in both cd and vinyl playing. If only in vinyl, you will probably need a subsonic filter, as I said before. You can always build an isolated floating table, as I did, or buy a TT platform designed for high tech precision instruments at around $5K😳. Please keep me informed. I would like to know what solved your problem, if you find the culprit.

Another thought, you may have a bad crossover in your speaker, but that would have to be both speakers failing and that’s very unlikely, but virtually everything you’ve described makes no sense. Don’t get the wrong idea-I believe you, it just doesn’t add up. You’ve invested many hours in posting and trying suggestions.  I feel your pain. Pls try a filter.  If that doesn’t work, you must be in the Twilight Zone.  No disrespect intended. It’s just too crazy.  🙃

O_holter: Sorry I misunderstood you, conerning the bump during cd playback.  Since it's only when playing vinyl, common sense dictates it has to be in your TT.  Too bad u don't know someone who could bring their TT over for an A/B comparison.  Good luck. I'll be very interested to know what u find.                                                 Steve in Tennessee.