I noticed this same problem using fig2eps. I found that in this case,
telling it to use dvips to compute the bounding box makes it work. This
doesn't appear to be an option for eps2eps though... So it would seem
that it is a ghostscript issue.

-- 
eps2eps fails to write the correct bounding box -- new bug in Gutsy, worked in 
Feisty
https://bugs.launchpad.net/bugs/156295
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