mod_perl should not require changes

This is almost completely not true. mod_perl is very different from running a command line perl script. As was mentioned in other responses your working directory may not be what you think it is, and depending on how apache is set up, it may even prevent you from doing a chdir().

Not to mention that you are now running in a persistent environment where the difference between compile time and run time are even more significant. This will also magnify other problems in your code (globals, unintentional closures, etc) that would not show up otherwise.

All of these issues are known and well documented and acceptable if you want the performance benefits of mod_perl. But to say that it shouldn't require any code changes is very misleading...

And for the OP, you can read here for more info on begining your mod_perl life.