Hi, Carla,
Whether the account-department codes are being read from the Job, Phase or Category depends on the Revenue Tracking Level defined on the Job record. You might be checking the Job record accounts, when really you need to be checking the Phase or Category record.
Also, if the account-department code fields are blank on the Job, Phase, Category record, then this information will get read (default) from what is defined within the Company Profile, Accounts tab.
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Regards,
Softrak Tech Support