How can the fact it's TCP/IP interfere with the tones? TCP/IP only sees bytes.
I doubt you'd be able to plug a dial-up modem into skype and achieve a working computer connection. Pure tones (as from key presses) is a less extreme case, but it's a conceivable problem.
There are also issues with the echo cancellation Skype uses. If you have issues with DTMF, that's the likely cause, not the audio codec.