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Reconcile crashes the application when a large number of modifications have been performed in the origin or destination relationship class for the version being reconciled.
Internally during the reconcile process the geodatabase creates a keyset table used to store the origin or destination primary/foreign key values for quickly traversing the attributed relationship class. If the number of modifications in the origin or destination attributed relationship class for the version being reconciled exceeds 200 objects, uninitialized memory is referenced and the application crashes.
Apply the ArcGIS 9.2 SP4 Reconcile patch available on ESRI Support Center.
Patches and Service Packs - ESRI Support