> Is there anything I may be missing about the general configuration or 
> environment of mod_perl which may be causing this strange situation?

Try profiling...

Some time ago I found my modperl app to be fairly slow because I
turned on use Carp (and was carping errors and warnings). After
disabling carping it was almost 10 times faster. I have also found
that SWIG generated interface to some C++ library is very inefficient
in some places (especially destructing a lot of objects) and manually
written XS module happened to be a few times faster (it was the case
with a lot of small objects). I think there are also other similar
potential problems...

-- 
( Marcin Kasperski   | Most of the bad things that can happen to a project   )
( http://www.mk.w.pl |     are the result of miscommunication. (Booch)       )
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( Porady dla programisty Oracle: http://www.mk.w.pl/porady/porady_oracle     )

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