As suggested I removed the nvidia-glx and nvidia-kernel-1.0.9629
packages, and although wasn't lucky and ended up without X (I don't know
how that could have been avoided) I have managed to reconfigure things
with the ubuntu packages. Software update has run a few times now
without the error. Thanks for the help, and sorry for the hassle!
** Changed in: update-manager (Ubuntu)
Status: Needs Info => Rejected
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Distribution update fails
https://launchpad.net/bugs/84961
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