I am not as heavy as many of the other monks here reguarding apache or mod_perl.
If it works fine as a .cgi it should work fine as a .pl, assuming of course it is a bonified perl.
I have worked with both cases. Make sure you have checked everything, however mundane before you blame it on perl, it's not the one configuring the web server.
Somethings things to consider:
- Again make sure your line in httpd.conf is correct: AddHandler cgi-script .cgi .pl
- Did you restart your web server after you changed the httpd.conf file?
- Make sure your .pl is in cgi-bin
- Is the permissions on the file correct?
I'm sure others could add more and I hope they will.
Gyro