While trying to track down any potential configuration issues that might be preventing incoming DTMF tones from working I found the document from 2talk.co.nz that documents the configuration settings for the SPA112 (the ATA I'm using). http://blog.2talk.co.nz/spa122.html
Some of the settings are different to those in the provisioning file, especially around the call progress tones and ring patterns.
I doubt they have anything to do with my DTMF problem, but how important are those settings to be correct? I'm not sure whether the provisioning file is correct or the document from 2talk.