[popcornmix]

Here's a 100MB sample mkv on dropbox, it's the opening titles from Blade Runner Directors Cut, 1080p/DD5.1. Audio starts at 13 seconds, however chirping is usually evident as the green tree is being traced line by line.

A second 100MB sample mkv (dropbox) - the opening titles from Blade Runner Final Cut, 5 audio streams: default TrueHD, DD5.1 and 3x DD2.0 - is even worse, though I'm not sure if the multitude of audio streams (including TrueHD) is a complicating issue. If you play it then cycle to the DD5.1 audio, stop it and restart playback with the DD5.1 audio, you should hear chirping from the outset.

I've copied your audio settings, set amplification to 30dB and played both samples. I'm using an Onkyo 606 receiver with headphones. Heard nothing like chirping.
Also tried with an LG TV (32LW450U), and didn't sport any chirping.

My guess is that the chirps aren't really being output (do you have another hdmi device to try?), but are being generated by your TV due to it not liking the signal in some way (e.g. the clocking).
There has been a fair bit of hdmi audio rework recently (mostly committed to master on Nov 7th). I did include some config options to switch between different schemes in case there were problems.

But really I need to know what firmware introduced the problem. Can you take the working xbmc image and try it with start.elf/fixup.dat from Nov 7th?
Try to identify the firmware that caused the quirks, and I'll be able to narrow down what tests to run.