You should keep in mind that when lexical variables go out of scope, the memory used by them is NOT reclaimed by Perl. This is an optimization, assuming you will use the lexicals again. If you don't want this behavior, you can explicitly set the variables to undef when you're done with them, which will free their memory.
Are you doing anything with subroutine references? It's possible to chew up RAM by using things like Error.pm's try/catch syntax if you aren't careful to avoid accidental closures.
You might want to check out the mod_perl guide for additional information on Perl memory management.
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