Geoprocessing Extract Data Task does not return any features.

Hello,

I created a geoprocessing service by following the Clip and Ship example. When I run the Extract Data Task from within ArcMap, I get a coordinate system warning but the resulting shapefiles contain the correct features. However, when I try and run the Extract Data Task from the REST web interface, I get the coordinate system warning but no features are in the result shapefile. The shapefile does contain the correct fields though. Does anyone know what the cause of this issue might be? Is this a spatial reference issue?

Thanks,
Rob