At some point since I wrote the iPhone Core Audio Getting Started post, a small bug in my AudioStreamBasicDescription on the multi-Channel Mixer input went from not mattering to making the output a garbled mess. Those stream descriptions are tricky devils!

To fix it, you need  to change the line.

desc.mFormatFlags = kAudioFormatFlagIsSignedInteger | kAudioFormatFlagsNativeEndian | kLinearPCMFormatFlagIsNonInterleaved;

to

desc.mFormatFlags = kAudioFormatFlagIsSignedInteger | kAudioFormatFlagIsPacked;

or

desc.mFormatFlags = kAudioFormatFlagsCanonical;

Ahh, pure, clean sine wave.