Where are you getting your parts and are you sure you're buying lower tollerance devices? Partsexpress, for example is selling normal components that any moron can buy from DigiKey or even get free if they call the disties for samples. There's nothing special about their components despite their claims of "audio-grade".
The frequency response of a simple RC lowpass filter is defined by:
1/(2*pi*R*C)
Precision refers to the manufacturing tolerance of the process. A 100 Ohm resistor with a 5% tolerance means that anything +- 5 Ohms from 100 is allowed to be sold and anything more is discarded (or more likely sold as a 10% piece). By swapping the components, you change the frequency response of the filter. Any difference in the sound you hear is due to the fact that the filter is responding to a different frequency.
If you want a steeper negative gain to your filter, you'll have to employ a different circuit, not merely change your frequency response.
