I'm able to reproduce it using my backups. It seems to be related to the
volume levels, as you've suspected.

== Trials ==

Conditions:
Time A ... configuration from where I filed the bug
Time B ... configuration from my post where I haven't  been able to reproduce 
it anymore
Config file V ... config file of vlc ($HOME/.config/vlc/*)
Config file P ... config and state files (incl. volume levels) of pulse 
($HOME/.pulse/*)

So let's mix these. First trial period consists of all the possible
combinations:

AV+AP: noise
AV+BP: noise
BV+AP: noise
BV+BP: no noise

However, using the new config BV seems to alter something important in
P:

1) fire up BV+AP, result: noise
After vlc started, the pulse config/state file 
657b92791ebe658fba9f363b4ba14252-stream-volumes.tdb has changed
2) Now firing up vlc yields some very subtle noise at the very begin of 
playing, but overall 'no noise'.
3) Afterwards there's not even subtle noise at the beginning

I've attached both versions of the stream-volumes.tdb

== Conclusions ==

Looks like pulse has ceased to run fine with some stream-volume settings
which it had set on its own in a previous version.

== Messages ==
Observation unrelated to above's trials:

The following message is shown on console independent on whether there is noise 
or not:
[aac @ 0x1b63650]Transition from an ONLY_LONG or LONG_STOP to an EIGHT_SHORT 
sequence detected. If you heard an audible artifact, please submit the sample 
to the FFmpeg developers.

** Attachment added: "stream-volumes in A condition (old setup with noise)"
   
https://bugs.launchpad.net/ubuntu/+source/pulseaudio/+bug/772720/+attachment/2122755/+files/A_657b92791ebe658fba9f363b4ba14252-stream-volumes.tdb

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https://bugs.launchpad.net/bugs/772720

Title:
  extreme noise with sound

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