Hello,
I agree, coordinate systems seem to be a likely culprit. It's probably worth checking the coordinate systems of the JTX_JOBS_AOI feature class and of any MXDs that your jobs use, just to make sure that they are what you intend them to be.
Beyond that, how are you defining your job's AOI? Are you using the "AOI" tab in the WMX Application, the "DefineAOI" custom step as part of a workflow, through a web application via WMX Server, etc.,?
Also, how are you viewing the AOI after it has been defined, and are there any viewers that "agree" with each other? For instance, if you view your AOI in 1) the WMX AOI tab for that job, 2) the WMX "Map view" for a job query result, and 3) ArcMap (by adding the "JTX_JOBS_AOI" feature class from your WMX database), how do the AOI positions compare with each other and with the polygon that you originally entered?
Brian D.