We have a GP service that has been running in production for a couple of years successfully with ArcGIS Server 9.3 in a distributed Linux/Java SOM/SOC environment running on Redhat Server 5.3 using shared SAMBA/CIFS mounts for the working jobs/output/cache directories.
When moving ArcGIS server to 9.3.1 sp2 we areseeing an error#999999 when executing from the REST interface.
After a bit of playing around we have established that the GP service only fails when the work directories are mounted from CIFS. When I changed the location of the working directories to GFS from the CIFS mounts it works with no errors. It also works fine with a single SOM/SOC machine using the local filesystem.
Initially we were using Samba 3.0.33 but are seeing the same errors when using Samba3x and when using shares from a Windows 2003 Server.
Besides the error#999999 we are not getting alot of feedback. The service appears to be failing at the point we expect it to connect to the DB through a direct connect file.