I noticed that the onboard PCI was marked as busy in the log, and that
there was a systemwide pulseaudio daemon running. The contents of
/etc/default/pulseaudio (minus comments) is:

PULSEAUDIO_SYSTEM_START=0
DISALLOW_MODULE_LOADING=1

But somehow it seems to start pulseaudio on boot anyway.

Killing the systemwide daemon manually (as /etc/init.d/pulseaudio stop
does not work, since it believes it is in "per user" mode) and
restarting my local pulseaudio enabled the onboard audio.

I could not immediatly see where pulseaudio was started from. References
to pulseaudio in /etc:

/etc# find . | grep -i pulse
./pulse
./pulse/system.pa
./pulse/daemon.conf
./pulse/default.pa
./rc1.d/K15pulseaudio
./rc5.d/S50pulseaudio
./default/pulseaudio
./rc3.d/S50pulseaudio
./init.d/pulseaudio
./rc2.d/S50pulseaudio
./rc4.d/S50pulseaudio
./dbus-1/system.d/pulseaudio-system.conf
./xdg/autostart/pulseaudio-kde.desktop
./xdg/autostart/pulseaudio.desktop

Any ideas where it might be started from?

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https://bugs.launchpad.net/bugs/914808

Title:
  [Realtek ALC888] Pulseaudio fails to detect card

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