Because your fingers aren't doing anything on the touch screen when you are in the middle of a call, the CPU could be slowing down to it's lowest set clock speed.
What is your CPU min frequency set to? I don't know about VOIP, but I've heard about sound quality issues with music playback with it set to 100MHz. Try upping it to 200 MHz if it is.
The only other thing I can think of is network speed. If using mobile data do you have a good 3G connection? If using WiFi then do you have it set to save power when screen off? (Screen off by proximity sensor during a call probably wouldn't put WiFi into power saving mode anyway I don't think)
That's the best ideas I can come up with I'm afraid
If this doesn't fix it then go ahead and try a different baseband or kernel, it's quick and easy to do...
Sent from my GT-I9000 using Tapatalk