The target layer/table is dropped from the map service when a map document containing a join and consuming data from a file geodatabase stored at a shared location is published to ArcGIS for Server that has directories located on the same network share.
Duplicate of BUG-000095875: This bug is fixed in the ArcGIS for Server Publishing Patch, available for download from the following link, http://support.esri.com/download/7397.