Here is my guess (purely a guess) on where to look for the problem.
Clearly a hook is being called on return from S3 and on return from S4
to fix the state of the audio device. On return from S3 (suspend) the
hook does the right thing. On return from S4 (hibernate) the hook is not
doing the right thing. Doing a suspend/resume after the hibernate/resume
is clearly re-initializing the hardware correctly so we know the S3 hook
does the right thing. Have a look at what is different between the two
hooks and you will find what is wrong here. I would look at it myself
but although I hack kernels in other OSes, I've never touched Linux
internals.

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Sound problems on hibernate, IBM T41
https://bugs.launchpad.net/bugs/98605
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