I'm not sure what you've tried or what your expertise is but....If this problem involved analog Zap trunks you may have a DTMF level issue which could be adjusted, if it was DTMF from the inside to the ivr's it could be a level issue on the sip phones. DTMF inband and out of band can have different issues at different points in the call chain. The IVR's rely on getting real DTMF audio from somewhere. If you call out to a plain POTS line and then press DTMF buttons what do you hear? Possibilities are nothing, very short tone, double tone, distorted or low tone. If you hear a tone is it on depression of the key or when you let off, does the timing of the press make a difference.
You really have to be able to listen to whats's happening or when thats not possible review either CLI traces or become familar with and use a tool like Wireshark which would be my choice right now. Its ability to capture whats happening is second to none. if your router or switch can be set to port mirror the asterisk port then you can use it that way. If not you can use a pc with two network cards or one hardwire nic and the wireless on your laptop or connect the asterisk server to a HUB and tap in that way. The computer running Wireshark has to be able to see the packets.
So understand that out of band DTMF (rfc8233) so to speak is the best option but when you dial out to and IVR somewhere its most likely that the IVR box will be looking for inband DTMF that has to be reliable supplied at the digital to analog conversion point.
brian
Phone System 