Are you retransmitting the signal from the 1st transmitter at the second transmitter, and is the MP3 from the second transmitter?
Like this:
First transmitter -> First FM receiver -> Stereo Tool -> Second transmitter -> Second FM receiver (second MP3 file)
If so, I guess your reception at the first FM receiver is bad. And with the noise filter set to 9, you will indeed loose some softer sounds - especially if the input volume is also low very. The noise filter can remove some noise, but that always comes at a cost.... Except for that, the stereo noise isn't a white noise signal, which means that the noise gate cannot distinguish it from the actual sound and hence cannot really remove it properly.
Even worse: By using the FM Soft preset, soft sounds (including the noise) will get amplified a bit...
By the way, if you REALLY want to do this (remove FM stereo noise and then retransmit - which is generally NOT a good idea), try my other program
Tape Restore Live!, which contains an FM hiss removal filter. See
http://www.hansvanzutphen.com/tape_restore_live/ . Given the type of stereo noise that I heard, I think you need to set the smooth/rough slider closer to rough. This program analyzes the sound and really separates FM stereo noises caused by bad reception from other sounds. And then removes them.