We've had some trouble with Query Layers being used in a GP Service.
The main bug we've used as tracking is this: NIM091142 -Unable to create geoprocessing service for a query layer referencing data in an Oracle database when the database is registered with ArcGIS Server
(however it is not specific to Oracle).
That said, the symptoms are usually that you cannot create the service using a query layer.
We have this bug fixed in 10.2 which should be released sometime this month. Will you have access to 10.2, will you be able to upgrade?