I've just uploaded a new version of Padre-Plugin-Debugger to CPAN. It has been stuck in github for a while as I meant to write some documentation and start calling it version 1.0. But as I haven't written any documentation yet, it is still just a puny 0.3 version.
The major update is how the interpreter is called. Now it will actually find the modules you are using, if you add the correct directories to 'Edit -> Preferences -> Run Paramerters'