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Users whose accounts reside in the EU or AP domains but whose managers accounts reside in AM or some other domain in the forest are not displaying their managers at all. Additionally these users are not showing up as direct reports of their manager. Of course the opposite is true, if your account is in AM or EU and your managers in AP you have the same issue. So if the user's domain differs from the manager we have this issue.

Is anyone aware of a fix or workaround for this?

We have the UPS created with each domain as a different synchronization sources. This is a multiple forest, multiple domain environment.

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I absolutely cannot believe the number of problems that were caused by this misconfiuration of AD. The domains in question had special permissions on the computers OU that hid the OU from standard users. This caused an exception in the UPS that was never found in logs.

For more details on how I managed to figure this out, please see the SO question and answer: Principal.IsInRole(“AD Group Name”) always returns false, no exceptions thrown

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