Interesting, I have to think about that one - I suppose there is something going on with resonance in the arm / cartridge relation, if without the silicone damping the low double digit frequency response goes up. The SME 3009 III has a knive(s) vertical bearing, so unless there's something completely bad on those, we can rule that out.
One would have to use test records and get graphs at this point to investigate, at least here is a good source of great experts, I would put this in the respective threads, like:
Introcucing the Phono Cartridge Measurement Library
Phono Cartridge Response Measurement Script
This is, as I am sure you know - better addressed there, not really an issue of MM vs MI vs MC and I would think the people in the other threads are more often there, than here...
Edit: Now that we know it's an Aries 3 - that is an unusual setup with a SME 3009 III arm... I wonder if something is going on with the Aries bearing, that is making it's way into the arm. The silicone damping making a difference could point to that. I bought a Stethoscope way back when I worked on engines, the metal rod type - I still have it and use it, if I want to check bearing noise on Turntables. Might be worth to look into, these are cheap and worth it.