I may have missed it, but I didn't see any mention of whether the AV equipment makes use of the safety ground. Since this wasn't mentioned, most likely it does, however there is lots of AV equipment that does not use the safety ground. I don't know how likely it is that it would help, but if any of the AV gear is not using a safety ground, I would try changing that just to see what will happen. It can't hurt anything, and it will make the equipment safer. You have to replace the two-wire power cable with a three-wire power cable that has the safety prong on the plug. Obviously the safety ground wire (green) needs to be connected to the chassis of the device, but make certain that the point where you are thinking of connecting it is a true chassis ground, by using an Ohmmeter to read the resistance between that point and the outer conductor of RCA outputs. Additionally, not knowing how old your house is, if there is any chance that wall outlets aren't correct with respect to the safety ground, this should be checked and corrected if need be. I am not especially knowledgeable of house wiring, but my understanding is that the safety ground for each receptacle should have a good conductive path to the breaker box, using either a dedicated wire or else conduit if there is conduit, and at the breaker box, these should all be joined to the "neutral" conductor and grounded to earth. If this does not correct the problem, it still is worth doing, if any of the AV components is not already using the safety ground, for multiple reasons to include the fact that it will allow the isolation transformer to work better if this doesn't work and you need to add an isolation transformer. The isolation transformer should be the type that uses a conductive (faraday) shield to isolate the primary and secondary windings and it should be placed as close as possible to the subwoofer so that the cable length between it and the subwoofer will be as short as possible.
Honestly I do not have a lot of knowledge in this area, and one thing that I don't really understand in your description of the problem is why disconnecting the safety ground at the subwoofer eliminated the problem.