Are you using a single print() under PerlEx? If not, try to use a single one (i.e.: buffer all output in a variable and send in one shot). I remember a buffering issue related to PerlIS in 5.8.x back in 2004/5 and it can only be mitigated with a single call to print. Multiple calls were creating some sort of error. And for the apache issue. I think if you did not compile Apache & mod_perl from source, we can't be sure if there is a problem in Apache setup or your code.
I only use single print in general because it is more efficient. As for apache/modperl, yes it was setup correctly since I used the PPM method of setting it up as suggested by modperl for activestate installations.
not to mention the apche one works fine with a few users but has issues with more..same as PerlEX is having.