Why are my woofers pumping?

@o_holter Reading over these posts I'd lean toward motor, pulley or bearing as the source of the problem.  By way of example, a couple years ago I noticed excessive woofer pumping in my speakers.  It was extreme to the point where I could hear chugging from my subwoofer.  I have a VPI HW-19 Mark IV with a very early SAMA.  The early SAMAs came with a flywheel that was a large stainless steel washer that just slipped over the motor shaft.  Upon examination I noticed that this "flywheel" was wobbling while the motor was running.  I removed the flywheel and the problem was solved.  I later learned that VPI eventually realized the flywheel was causing more problems than benefit and discontinued using it.

Since you observed much less pumping after removing your platter it sounds like either your platter was out of balance on the bearing or the bearing was not properly seated.  I would clean the bearing shaft with long qtips and reoil the bearing shaft with a high quality oil.  I use sewing machine oil.  Second, I'd examine the pulleys and motor shaft for any wobble.
Cheers,

If I were you, I'd start from square 1....make sure the cartridge suspension and stylus is ok.   I'd send it back to Lyra for a checkup.  They probably won'r even charge you to look at it.  The Atlas is one of my favorite cartridges....I've heard it in  V with a high end system with powerful low end and no woofer pumping.

>>>>>> I can see it, even if I don’t hear it. Why does it happen? The woofers behave normally (no pumping) with digital music, and when the stylus it lifted from the groove, so it is not the speakers, amps, preamp or phono stage. <<<<<<

In the day of phono only they had a button sometimes labeled "Rumble filter."  That's what you got.  Others may say "Low filter."  Interaction between the cartridge, tonearm and record cause ir.

Does your turntable have an attached cover? If yes, it catches low frequency audio like a sail catches wind. See if removing it reduces the feedback. If yes but you still  want to keep the cover attached, rotate it perpendicular to the speakers to at least reduce the pickup. Worked for me! Just a thought. - Andy

Whatever you do, don’t get a subsonic filter, unless of course you want to kill good sound.

This is nonsense. I use the cheap DB Systems filters and the loss in fidelity is barely perceptible.

I also discovered that, indeed, "silent" record grooves are not the same.

You discovered that subsonic noise is often cut into the grooves. This is why you're not getting pumping in the runout grooves. I once believed warps were the major culprit. They’re not. It’s usually acoustic feedback and poor album cuts

Read some of the reviews on these:

http://store.acousticsounds.com/d/60042/DB_Systems-DB_Systems_Subsonic_Filter-Turntable_Accessories

At only $20, it can’t hurt to try them. If you like the result, consider investing in the DB-12 or KAB filter.