Yes, you can run the JTX Custom post outside of ArcMap by using the JTX GP Tools. These GP Tools are not exposed by default at 9.3.1 but will be at 10. You can add them by creating a toolbox in ArcCatalog - http://help.arcgis.com/en/arcgisdesktop/10.0/help/index.html#//003q00000010000000.htm After creating the toolbox, right click and choose add tool. In the dialog, you should see JTX Tools. Go ahead and check the tools that you want to use, I usually just enable everything. You can run the post tool by passing in a job ID and specify a JTC file. If no JTC file is specified it will use the default JTX database on the machine it is currently running on. With the LaunchGPTool step type, you can plug this into your workflow and run this on your Job by using the [Job:ID] token.