I'm wondering if you are maybe seeing this from the wrong perspective?: If the entire wall is now vibrating in sympathy with a nearby noisy fan, then that means it is NOT coupled to the floor! It was before (which is why it didn't vibrate so much, as it was being damped by the floor: it was transferring most of that energy to the floor), but now that it is properly isolated, it can vibrate freely, like it is supposed to do, since it is NOT connected to the floor any more...
and can only conclude that the existing, outer walls transmit less of the attic fan's vibrational energy than my new, isolated inner walls (the open framing, anyways).
Right! ... Sort of... Because your outer-leaf walls are still fully coupled to the outer-leaf floor, those walls vibrate less, apparently, but that's because they are transmitting MORE energy to the floor, not less.
That might be one explanation, assuming that the issue is airborne sound from your fan, not structure borne. However....
The inner walls don't have drywall or insulation yet
Ahh!

Then they most likely are not floating properly yet. The Isosill stuff is designed to work under the compressive load of the entire wall weight. Right now, you only have a bit of framing on there, not the full load of the finished wall. Once the wall is completed, the full load will be compressing the rubber to the optimum point, and the wall will float at its best.
On the bright side, if I put my ear to the inner wall and hit the outer wall with a hammer, there is very, very little noise transmission.
Bingo! That shows it is decoupled. Maybe not as fully as it will be when the full load is on it, but even so it is decoupled.
So, maybe my new framing members are sympathetic to the attic fan's vibrational energy?
That would be my guess.
Should I just move on and complete my inner walls then?
Yup! I'm betting that as soon as you get the first layer of drywall on there, even just a few sheets, that resonance should go away, or at least drop in intensity. Right now you are trying to measure the effect of an incomplete system, but MSM only works when all the parts are in place. It's like you were trying to test how your car's suspension is working, but you only have the bare chassis, no engine, no shock absorbers in the suspension (only springs), and the tires are only half inflated! You won't be able to discern anything at all about how well the car will ride once all the parts are in place.
So I would say don't sweat it too much: just go ahead and build!
- Stuart -