Apologies, there was one more (possibly relevant) dmesg line I missed from my 
previous comment:
[   11.165206] HDA Intel 0000:00:14.2: irq 24 for MSI/MSI-X

A random thought occurred;  I know very little about this sort of thing
and so this is possibly a complete red herring:

[    1.832519] ata2: SATA max UDMA/100 mmio m...@0xc0004000 tf 0xc00040c0 irq 22
[    1.833418]   alloc irq_desc for 16 on cpu 0 node 0
..snip...
[    1.833431] pata_atiixp 0000:00:14.1: PCI INT A -> GSI 16 (level, low) -> 
IRQ 16

Could these lines in the dmesg be indicating that there is some
unwelcome interrupt sharing going on?  It looks (to the untrained eye)
like some of the IDE or SATA is being mapped to IRQ16 along with the
audio.

The reason I mention it is that I also have a bug open for intermittent timeout 
issues on the SATA controller:
https://bugs.launchpad.net/ubuntu/+source/linux/+bug/382812

As I say, probably not relevant, but mentioned in the interests of
completeness.

-- 
[karmic]snd_hda_intel: audio moves to polling mode and starts repeating 
(Toshiba A100-259/ATI IXP SB4x0 HD/ALC861)
https://bugs.launchpad.net/bugs/391114
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