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:

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.