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Yes, I have fixed this problem and now understand how it works. Basically if any GIS Resource (mxd, or shapefile referenced in an mxd is NOT ON THE soc machine, then you need to go to the machine where the GIS resource is located, and do the following:
step 1: Create what I call a 'mirror' ArcGISSOC local user account on that machine (called the remote machine because it is remote to ArcGISSOC); Make sure the spelling is IDENTICAL 'ArcGISSOC' and the the password is IDENTICAL.
Step 2:
Find the folder(s) where you have SHP and MXDs and make shared directory on those folders.
Add this new local user account ArcGISSOC to the PERMISSIONS of this share, READ ONLY is enough.
For Shape files, also press the SECURITY pane and add ArcGISSOC to have security access (read-only is enough) to the folder that has shapefiles. Make sure you apply to subfolders if you have a hierarchical directories of shapefiles.
Step 3:
Open MXD files you wish to publish. Ensure that ALL shape files are using UNC path - you will have to add your own login id to the share permissions too. You will have to change the data source location from C:\... to \\myshpshare\... then Save MXD files.
Step 4:
Open ArcCATALOG as your own login id or Run As login id that you know is in agsadmin.
Step5:
Publish MXD via the UNC path name.
Step 6:
Test preview geometry - if this fails, then your shape file is not accessble by SOC and check your UNC share information.
Let me know how this goes....
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