It seems somewhat counter to logic to purchase a subwoofer that now requires a rumble filter. If you can "hear" the subwoofer operating during normal playback, that typically indicates the level is set too high; turn it down a bit and see if that alleviates your intermittent problem. Someone else mentioned this. But as a matter of fact, 30 and more years ago good receivers and integrated amplifiers often did come with rumble filters. They went away with the purist movement of the late 80s and 90s and possibly the realization that there was more profit to be had by not incorporating a rumble filter. Do you perceive that the diaphragm of the subwoofer or your main speaker woofer is "pumping" when the problem is occurring? In that case, and after you have exhausted the possibilities of re-arraging your components (see below), a rumble filter might help.
Your problem can also be due to placement of the components in your listening room. Low frequencies can produce standing waves that contain quite a bit of energy which can induce physical movement of the tonearm/cantilever, generating spurious low frequency interference. Where is the tt with respect to the sub woof? Try moving one or the other and see if that affects the problem you are trying to solve. Someone else mentioned this, too.
Do you really know for sure that the sub woof is the culprit? Does the intermittent problem disappear when you disconnect the subwoof and run the main speakers full range?
Your problem can also be due to placement of the components in your listening room. Low frequencies can produce standing waves that contain quite a bit of energy which can induce physical movement of the tonearm/cantilever, generating spurious low frequency interference. Where is the tt with respect to the sub woof? Try moving one or the other and see if that affects the problem you are trying to solve. Someone else mentioned this, too.
Do you really know for sure that the sub woof is the culprit? Does the intermittent problem disappear when you disconnect the subwoof and run the main speakers full range?