Those latencytop numbers seem very healthy to me, but I'm not an expert
with latencytop.  When you run latencytop, make sure the audio
application is selected on the bottom half of the screen.  Since your
system as a whole seems fairly responsive, the top half of the screen
(overall system) is less important than the bottom half of the screen
(the selected application).  You can check "vmstat 1" or "top" to see if
anything is running in the background.  You shouldn't get audio
stuttering from a modest system load, unless one of the apps is
misbehaving.

This may be a hardware driver issue for something that is in the docking
station (possibly not the audio driver).  You might compare "lsmod" when
you boot up docked versus undocked, to see if there are additional
modules loaded for one configuration (also lspci, etc).  It sounds like
the "bad" driver isn't being loaded when you boot up undocked.  You can
also try "dmesg" instead of /var/log/messages, which sometimes gives
more detail.

When you boot up in/out of the dock, are you doing a cold boot, or could
this be related to suspend/resume?

-- 
Rhythmbox stutters with no system load at all
https://bugs.launchpad.net/bugs/330398
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