Christina Phillips found another oddity in the GP Reconcile to GL functionality. I’ve found plenty of them too which is why I push The Closer so much. Frankly, it not only does more, it’s better quality product for reconciling subledgers to GL.
Dynamics GP Land: Reconcile to GL Oddity
Archived post from 2011. Dynamics GP and the links it points to have changed since; check current documentation before relying on version-specific steps.