Fist a note: the problem was not found in mkisofs but in genisoimage.

The problem has however been in mkisofs too and as genisoimage is just
a very old version of mkisofs, it suffers from the problem.
While mkisofs did fix the related problem by rewriting major parts of the 
code in October 2006 (this is before genisoimage was released), there is no 
fix available for genisoimage.

The best solution is to download the latest version of the original software
from http://cdrecord.berlios.de/

-- 
genisoimage error "directories too deep" using Rock Ridge
https://bugs.launchpad.net/bugs/135362
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