I have a simple workbench script that uses a SystemCaller to run a batch file, then checks for success/failure. It runs fine through workbench when logged in using the FME server user, but not when published and run through FME Server.
In FME Server the job looks like it completes successfully (return code 0, no warnings/failures), but it doesn't actually execute the instructions of the batch file. Since there is no error message in the log, there's not much to go on for diagnosing the problem. It isn't due to a path problem because the caller fails if I give it a bogus filename.