I can confirm that removing .pulse directory does *not* solves the problem for 
me  :-(
But I found an empirical solution that is perfectly reproducible for me and 
maybe can shed some light on the problem:

1. start playing an mp3 with VLC -> sound is distorted/crackling
2. while VLC is playing, kill pulseaudio with 'pulseaudio -k'
3. obviously VLC is not happy and crashes
4. restart VLC and... voilĂ .. the sound is perfectly clear from now on, even 
after suspend/resume cycle !!!

Note that simply killing pulseaudio withouth VLC playing does not work
(at least for me).

This trick also solves the similar audio crackling problem with Skype new 
version which was unusable for me before!
Maybe there is a problem of pulseaudio initialization for some applications?
Or could this be related to DMA/Buffer issues of the specific soundcard/codec 
(like position_fix or irq workarounds you see int the attached dmesg) ?

lspci | grep -i audio:
00:1b.0 Audio device: Intel Corporation N10/ICH 7 Family High Definition Audio 
Controller (rev 01)

cat /proc/asound/card0/codec#0 | grep -i codec:
Codec: SigmaTel STAC9200

dmesg | grep -i hda:
[   25.363052] HDA Intel 0000:00:1b.0: PCI INT A -> GSI 21 (level, low) -> IRQ 
21
[   25.363057] hda_intel: position_fix set to 1 for device 1028:01cc
[   25.363123] HDA Intel 0000:00:1b.0: irq 46 for MSI/MSI-X
[   25.363157] HDA Intel 0000:00:1b.0: setting latency timer to 64
[   25.479947] input: HDA Intel Mic at Ext Left Jack as 
/devices/pci0000:00/0000:00:1b.0/sound/card0/input8
[   25.480224] input: HDA Intel HP Out at Ext Left Jack as 
/devices/pci0000:00/0000:00:1b.0/sound/card0/input9
[   32.464729] hda-intel: IRQ timing workaround is activated for card #0. 
Suggest a bigger bdl_pos_adj.

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https://bugs.launchpad.net/bugs/751265

Title:
  pulseaudio distorts VLC audio

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