Even though I did start with the recommended loading values set by the manufacturer
They specify those lower loads because they have no idea what phono section will be used and the simple fact is that many designers do not take the electrical resonance I mentioned earlier into account. This causes them to be sensitive to RFI and thus the loading resistor has a very noticeable effect.
But nothing comes for free except nothing and sometimes you have to pay even for that :) In the case of a loading resistor, 100 Ohms is 2 orders of magnitude less than 47000 Ohms and so you are asking the cartridge to do more work driving that load and so the cantilever becomes stiffer (less compliant) due to the electrical load. This can have an effect on how it behaves in the arm.