I was trying to test my Asterisk dialplans with Ekiga on my Ubuntu m/c. There is an excellent write-up on this here. Following the steps Ekiga registered to my SIP account without much trouble.
But I found Asterisk was not reading the inputs from Ekiga, like the extension number or options for the IVR. To solve this problem I went to Ekiga - Edit -> Preferences -> Protocols -> SIP Settings. And changed the DTMF MODE : Send DTMF as to RFC2833.