It could be that the script is relying on files that are in the @INC path when run from the command line and not when it is run by a service. In other words are there module or configuration files that the scripts need to run that aren't in the path for the service.
If this is the case there are at least two options.
1) add a use lib "/path/to/modules" in the script
2) move the script and dependent files into a path in the @INC for the service.