I am confused. A 100uH and 1nF filter has a cutoff frequency of 503KHz, so am not sure how it can affect your audio.
You also mentioned CW, and CW works directly on the unbalance of the mixer and does not come near the audio circuit, therefore I can't understand how it affect you power out.
Are you sure there is not something else?
Also I placed the low pass filter on the input of the SSM2167 module (if you still have it in-line).
But either way it should not affect your power out.
All the best,
73, John (VK2ETA)