Something is badly wrong with the set of prototypes in your question bank: either some have been moved into incorrect contexts or multiple copies exist. Three important questions:
- Does this problem occur with all question types or just c_program?
- Is this a newly installed CodeRunner plugin, or is it one that used to work?
- If the latter, do you know if anyone has edited the set of prototypes?
The most likely explanation is that someone has managed to create multiple copies of the prototype for the c_program question type (and any others that are failing), in which case you'll have to hunt down the duplicates and delete them or change the question type that they define. The section User-defined question types in the documentation is important here.