Our investigations have shown that this is a result of a gpLink attribute on the Organizational Unit being in the state "<not set>".
In order for Block Inheritance to work, the Block Inheritance flag must be set and the gpLink attribute must be set to some value.
In the case of the Organizational Unit in question having at least one object linked to it this behaviour will not be observed.
In the case of the Organizational Unit having no objects linked to it, Group Policy Management Console will change the gpLink attribute from "<not set>" to " " (a single space). This enables Block Inheritance to work correctly. GPOAdmin is not currently changing the gpLink value from "<not set>" to " " which is why Block Inheritance is not working.
To correct this, either link an object to the Organizational Unit or change the value of the gpLink attribute on the Organizational Unit in question from "<not set>" to " " (a single space).
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