I have to self compiled Kernels on a Debian Wheezy System. On * Linux debian 3.5.1-custom01 #1 SMP Tue Aug 14 19:42:16 CEST 2012 x86_64 GNU/Linux the described problem isn't existing. On my Second Kernel * Linux debian 3.6.0-rc3-custom01 #1 SMP Thu Aug 23 17:45:40 CEST 2012 x86_64 GNU/Linux I have the problem, that all sounds I play are very noisy for example when playing music using Juk on KDE. The Default Backend of KDE was VLC with which the Problem in connection with 3.6.0 exists. When I change the Backend to GStreamer the sound is normal. I then looked for the Problem in VLC. It turned out that within VLC only the ALSA Audio Output works correctly. The other modes, namely Standard, Open Sound System, Pulseaudio and Audio Memory Output are noisy. I compiled the two Kernels the same way but the problem only appears on 3.6.0
Does the problem still happen with 3.12 kernel? If yes, please give alsa-info.sh output. Also, you can try to pass position_fix=1 or position_fix=2 option to snd-hda-intel driver. Try snoop=0 option, too.
I was not using debian for a long time. What I can say is, that I have never had such a problem with my actual system. * Linux manjaro 3.4.69-1-MANJARO #1 SMP Wed Nov 13 18:29:58 UTC 2013 x86_64 GNU/Linux