Yes, we are seeing this too. We use inphonex.com as our VOIP provider, and have our system using via VOIP only.
The answering attendant was working fine (for a few months) until about a week ago (when a customer emailed us asking what was wrong with our phones), now DTMF is not being recognized at all. I went to the support FAQ and found a section on the DTMF issue (related to using a voice modem), which recommended reducing the outbound messaging volume. I tried this, but it did not solve it. Using the call simulator, the system navigates fine. It's odd that it was working without any problems and then suddenly stops without any changes from our side... We have also rebooted the server, and reloaded the IVM application to no avail.
Anyone else have a suggestion of where to go next?