| Are you using the plugin within a DAW or as a standalone plugin?
And always always always, you're better served by doing multiple passes with less noise reduction. If you're, say, taking off 12 dB in your initial pass, try reducing that to 8 and then do another pass.
Keep a sample of the 'train' section you used on a separate track for easy reference (or set up markers for the section).
ALSO---I find I get much better (though takes MUCH longer) using the C-offline algorithm. If you think about it, you're asking the software to make the changes in real-time if using Algorithm A. I find it better to let the software analyze everything more in-depth and process it if I have the time to walk away for a bit.
Additionally, using the spectral mode can work WONDERS because you can see in a nice waveform/spectrogram display and also LOOP JUST THAT FREQUENCY/NOISE. But it sounds like you are using the plugin within editing software (pro tools?).
And then there is the old argument: if you are making up gain anywhere, do you reduce the noise BEFORE or AFTER raising the gain of the file/section?
-Jeff
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