Hi Suresh,
Something sounds wrong here. The creation of a Customs Shipment for Transit, and Declaration before GR are mutually-exclusive in the system. If you are finding the Inbound Delivery in the "before GR" work-list, then that implies that you have set that flag for the Delivery Type in the Plug-In configuration.
If that's the case, then clear that check-box and your preliminary document should then work properly for Transit.
Regards,
Dave