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what are the coordinate systems (and more importantly underlying datums) of the two services?
how could you judge alignment until you were overlaying two different services?
i could be wrong, but i doubt that version compatibility is the problem here.
ahh! thanks for clarifying 🙂
if thats the case, the same misalignment should appear in the REST service's JavaScript Viewer and even in the map document used to publish the service.
can you confirm whether or not that is the case and check the coordinate system of the actual data?