It sounds to me like the 'junction box' is on the side of the building with the service. Since 250.32(B)(2) applies to _detached_ structures, it seems to me like you would have to run an equipment ground to the junction box...which on re-reading your original post seems to be the problem.
Remember that the only time you can run a subpanel like a 'service' with bonded ground and neutral is if the subpanel is in a detached structure with no metallic pathways between the two structures.
-Jon
