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** This issue is addressed in ArcGIS 9.0 Service Pack 3 (SP3) **
If a relationship between two newly created features is established in a disconnected editing session, that relationship will be broken when the data is checked in when the following is true: the Relationship Class is Composite, and the Foreign and Primary Keys are user created attributes.
The relationship is broken because the Foreign Key value for the new feature is changed to the ObjectID value assigned to the related feature in the origin feature class when the data is checked in.