I've had similar problems before.

We will need more details though; is this your own Perl handler, an Apache::Registry script, or something else?

Have you tried testing your pages while running Apache in single process mode (httpd -X)? What happens?

Also, make sure you have read this:
http://perl.apache.org/docs/1.0/guide/porting.html#Sometimes_it_Works__Sometimes_it_Doesn_t

How are you generating the response headers? Apache::Request? CGI.pm? Do you "use strict" and "use warnings"? Check for any "will not stay shared" warnings and make sure you don't use "my" variables in a subroutine that were declared outside of it.

Finally, you may wish to try setting "Pragma" and "Cache-Control" headers.

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