On further investigation, the Ubuntu-Feisty version of genisoimage (9:1.1.0-1) 
running on edgy also does not have this problem!
I understand genisoimage is a fork of mkisofs now used in preference to mkisofs 
in etch and edgy.
I.e. This problem is edgy specific as far as I can tell!

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mkisofs doesn't properly convert lower case filenames to upper case
https://launchpad.net/bugs/70098

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