If you do an outbound call (i.e. outside Skype, to something that would actually use DTMF) Skype doesn't use SILK/Opus on the outbound connection. You can tell

If you do an outbound call (i.e. outside Skype, to something that would actually use DTMF) Skype doesn't use SILK/Opus on the outbound connection. You can tell because the quality is way worse. 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.