Ever see the Blue Man Group? Their most performed show is called, "Tubes." And a good portion of it makes use of the fact that the resonance frequency of a tube changes based on the length, like slide trombones, except made out of PVC piping and generally much lower frequencies.

Anyway, the point of the story is that perhaps your muffler just happened to get installed at a nodal point that reinforces the frequencies from your engine such that you get the resonance really bad. Perhaps, all it would take, would be to move the muffler a couple of inches up or down the pipe so as to change the resonate frequency enough so that it no longer reinforces the sound from the engine.

Of course, I'm no mechanic and never took any physics beyond high school (AP level, but high school nonetheless) so I could easily be resonating out my ass here.