Then there's DTMF.. DTMF decoders HATE the high tone being louder than the low tone. With pre-emphasized audio and a "flat" receiver, that's what you'll get. In the telco world, this is called "reverse twist". Typical DTMF chips work over a 30dB range in amplitude.
If your DTMF decode shows any sensitivity to the level adjustment, you have "reverse twist". To fix that, de-emphasize before feeding the audio to the DTMF chip.

