1) Security. Any code placed in the config file will be executed with the same permissions as the script itself. This may or may not be a problem.
2) Ease of use. Perl typically isn't the easiest language to use for simple configuration options, unless you're already fluent in it. Theres no real reason to require the some what complicated ( compared to yaml, config::simple, etc ) syntax of Perl unless you really need it's power. And for a simple config file, it doesn't sound like you do.