1) the Atlas / SME V combo is very “receptive” in the lowest frequencies, and that in some resolving systems this may give unwanted effects like woofer pumping.
2) this is mainly a resonance problem, not a rumble or player noise problem (it does not change much, with different platter mats, damping or stabilizing the turntable, etc), and the first measure is to try to move the resonant frequency up - reduce the effective mass of the arm. This is only slightly possible on the SME V, but even small changes may help
3) the somewhat "over-eager" reception at the lowest frequencies of the Lyra/SME combo makes it even more important to correct any residual system noise, drive noise or rumble.
4) if the problem persists, try a rumble filter.
I will now try to decrease system noise – check the turntable, bearing, oil, feet, etc.
I wonder, even if the pumping is already reduced, would a filter be an idea anyway? Are my woofers straining too much, in the lowest bass? Is this prone to happen more, when the suspension of the cartridge is more worn?