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Besides shipping transactions, you have to check other modules as well if you use those modules.
e.g. if you use wip, you have to check for pending resource / material transactions
See http://erp-consultancy.blogspot.com/2008/03/period-closing-process-in-financials-in.html for some tips
Hope this helps,
Apart for Shipping Transaction, the Inventory Pending transactions aslo afeect the period close process.
when 'GMF Period Close Process for Process Organizations' request is submitted it checks for all pending transactions for respective process enabled Inv org. All Inv transactions are considered Receiving, Shipping, GME(WIP issue, WIP completion and returns as well).