Very interesting!
I assume DTMF works different internally (pure SIP enviroment) as the process works perfect, it's only when coming in via our ISDN that has the problem.
I have just ran the custom audio file through the link you provided in the first post and it picks up almost every digit and some letters!
I then ran through the short agent-login file and the net-target-destination file which is default to asterisk and it detects none
I need to see if I can find some way of removing the tones from the recording without disturbing the audio