I think I’ve nailed it.
Talk about a weird problem though. It seems to be a bug on Lion (10.7.x), but only manifests with certain hardware, and then only with certain bit rate settings.
Given the long running nature of the problem, it goes without saying (but I’m going to anyway!) that I’m very glad to have made progress and even happier to have what I think is a solution.
The latest builds of v1 and HD contain the fix.
My only concern is that of introducing any regression. The fix itself is minor (simply forcing the incoming audio streams to be a of a certain format) – but AVFoundation appears to behave differently on different OSes and mixes of hardware, and while I’ve done extensive testing here, it is possible that it doesn’t work on some other configurations.
If you find this build to be worse than what you currently had – would you please get in touch? That’d be “grand” :)