And I guess same disks did work once, and once didn't right?

This is very likely a kernel problem.
I will report it to linux kernel mailing list.

Everything else is unrelated I guess.

Now just try few times to boot with and without the CD and see if this
is related. Use same disk (probably a data disk)

I have seen such things here myself, but rare.

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gnome doesn't 'see' cdroms/dvds
https://bugs.launchpad.net/bugs/431055
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