Ok, here's my findings:
Full re-install of course fixes it. Tried the following first though:
1. Turn on gps, reboot, wipe cache and dalvik, reboot, no go.
2. Fixed permissions, just for the hell of it, no go. (Really didn't think it'd help but you never know I suppose.)
3. Turn on gps, pkill -9 zygote, no go.
4. Wipe data partition, and cache, reboot, and incall audio came back. While this is not the solution you want, at least you know where to start digging now. (Problem is a change made on data partition, not on system.)
Going to do a fresh install now to play with this some more. I'll report back.