Well definitively the issue is because the audio for the fax transmition is going through the transcoder. Is your Service Provider accepting just G729? Maybe you can try to force the calls that goes to the ATA to use G711 only!
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G729 is not being used it is g711alaw. Anyway on further investigation it doesn't seem to be a ATA / Fax issue. I believe it is a transcoder / dsp issue as now the exact same issue is happening with external calls going to CUE when transcoder is enabled.
It think it is either a one-way or two-way audio issue as when ever the transcoder is invoked the call connects and stays up but there is no audio.
Incoming calls to the fax and CUE were working at install a month or so ago at install after configuring the transcoder. I am going to try a reboot tonight and see if it resolves