Why are my woofers pumping?

The Atlas isn't harsh! Probably their preamps weren't set up properly!

The resonance is a bit high - 7 hz ish

That's on the low side. The window is 7-12Hz.

@o_holter This really sounds like a turntable problem to me! I've dealt with this a lot; I repaired consumer electronics for a living right out of high school, through college and beyond. If its once per rotation, its something to do with the platter and literally can't be anything else.
To prove this out, change the speed to 45 rpm and you should see the pumping speed increase with it.

@o_holter , if its happening once per revolution regardless of the LP, its a defect in the turntable. Could be a bad bearing (which is why I specified grease earlier, rather than oil), could be something that rubs on the platter or it could be the platter out of balance, and shifting on its spindle as it rotates.

The preamp is clearly off the hook. To test this I would simply borrow a turntable, it does not have to be expensive, just to try out.

Just as a FWIW- the digital recordings you made may not have the subsonic information that is pumping your woofers, so I would not use such recordings as the results might be inconclusive.
Have you tried greasing the platter bearing yet?

I would grease the platter bearing and see if that makes a difference. If it helps, I would consider replacement of the bearing unless grease is an acceptable lubricant.

The fact that its happening in time with the rotation of the platter (as you stated earlier) points to the platter bearing.

Since degree of pumping varies with the LP and repeats precisely with the record's revolution, drive problems probably is not much involved - confirmed by cleaning belts and adjusting the player - no big difference.

This comment really suggests an issue with the turntable despite the belt cleaning (which would not address something like this).

Electronics bandwidth is an issue too- your amps are full power to 1Hz. Most tube amps can't go anywhere near that low.

But I have similar bandwidth with both the amps and speakers at home, yet don't experience this issue. I am using a Triplanar, which allows for a bit of adjustment of the mechanical resonance by using multiple weights for the counterbalance. My 'table is different too.

Its true that some lathes can impart low frequencies to the LP, but that usually occurs between tracks and also at the end, where the carriage for the cutter head is advanced at a higher rate than during a cut. It sounds like you are getting this pumping during cuts on the LP, so I would rule out the LP as the source.

I would try applying a light grease to the platter bearing, to see if it shuts it up. If so, I would be thinking that the platter bearing is worn as normally a light oil is used.

The interesting thing is: it happens at certain intervals per revolution of the record (playing silent grooves between tracks). If I turn up speed to 45, the pattern is repeated, only faster. This seems to indicate that player rumble or drive problems are NOT the main issue.

Boy, that sure sounds like a drive issue to me!

But it sounds like this is mostly solved :)   I would put a drop of oil on the platter bearing for good measure...

Based on Atmasphere's advice, I also tried higher loading, going from 475 ohm to 121 ohm (not so easy on the Io, changing a jumper at the back). Result? Musicality: great. "Echoes" sounds a bit sweeter, more mellow. I realize, I am moved by the music - always a good sign. Is it also a bit duller, rolled off, or contracted? Not sure. Maybe a little. I will have to try the middle setting (243 ohm). Testing with the Hifi news record, I did not find any change in the resonance frequency, it is still down at ca 7.5Hz.

Loading should not affect the tonality of the cartridge, as essentially the loading is to prevent a resonance at very high frequencies from occurring by detuning it. If it made for an improvement, it means that the phono section is sensitive to RFI at its input and may have stability problems (but not the sort that cause woofer pumping).

In an ideal situation, the cartridge should be loaded by 47K. With low load resistances (like 100 ohms) the cartridge has to do more work, and that energy coming from the stylus motion means that the cantilever has to be stiffer as well. JCarr and I talked about this at Munich a few years ago.

Now you mentioned that you examined the platter bearing- did you lubricate it? If the platter bearing was dry, the simple act of removing the platter and reinstalling it may have gotten enough lubricant in place to result in the reduced woofer pumping. So the arm and cartridge combo not being ideal might be a complete red herring.

OK... what do you want to know?

@invictus005 To which part do you address the 'huh'?

@o_holter A simple way to decrease the compliance of the cartridge would be to load it. I would try 50-100 ohms and see how that works out.

Its not a sure bet- if you load the cartridge too low, its output will decrease, and in turn you phono preamp noise will be more audible. But its worth a try.

Damping would probably make matters worse; I would run it without damping and remove the little bit that runs in the damping trough to reduce mass, even if its only a little bit.

@o_holter 

Raul's suggestion that the cantilever suspension is failing could be an explanation, but the problem I have with that is the cartridge must be pretty new so this seems really unlikely.

I looked at the specs of the ARC used in the review; it cuts off at 10Hz. Your preamp, if still the Io, is only specced to 20Hz (at which point its within 0.25db, suggesting that it can go down considerably further). So its an unknown as to whether that's an influence. Your amps are full power to 1 Hz. I use similar amps in my system at home, but I don't get the woofer pumping, although that was a problem when using the SME5 and has not come back while using the Triplanar (which I see was used in the article you linked, so this problem may not have shown up).

A filter will introduce phase shift, and in a full range system such as yours, will be audible as less bass impact. So its probably best to solve this with elegance rather than brute force.

Atmasphere - you may be right. But Lyra does not warn, and web debate does not complain, using the Atlas on the SME V - so i wonder.

It might be that some of those debaters don't have the bottom end bandwidth in their systems that yours has.

I went from the SME5 to the Triplanar and that helped get rid of that problem in my system. The SME5 seemed like it was a higher mass arm than the Triplanar. 

Your cartridge has a compliance value that is too high for your arm.

You could reduce the effective mass. That can be done with different weights on the counterbalance (a heavier weight, closer to the fulcrum), lower mass arm or a lighter cartridge. If you are using a cartridge shim, I would replace it for one that is lighter.