<SNIP>
a) autorun trying to play CDs automatically
I guess I don't understand this. If you're simply referring to
the CD player being busy, I'm not running the CD Player while
recording.
<SNIP>
Yes, but the windowing system, like KDE, creates a process called 'autorun'
that looks at the CD once per second to see if I've installed a CD, so that
it can start playing it. That work that it does each second can cause xruns.
Gnome does something similar. Many of us were having that problem last year,
but I never discovered how to stop it. In KDE I just kill the autorun
process.
Fluxbox (and others I'm sure) don't do this, so you get fewer problems.
Good luck getting this debugged.