as far I can see is your problem because you are grouping in different ways.
. . .
SUM([Entry Amt]) as [Entry Amt]
GROUP BY [Entry No];
BUT Shipped Qty:
. . .
sum([Shipped Qty]) as [Shipped Qty]
GROUP BY [Entry No],[Shipment Date],PO,[PO Row],[Trans Mode],[Country of Origin];
The (correct!) grouping results can be seen in the QV-Listboxes of these two fields. If you want to see one uniqe value (494 times) in the "Shipped Qty" for the current selection analog to "Entry Amt" use same grouping.
Nevertheless the summing up in your pivot should be correct as your grouping is different but the count([Shipped Qty] ) is also 494. So it seems to me, that you do not "loose" records during your joins. But the only one who knows it exactly is you.
I used statistic boxes (also for "receipt qty" and "order qty"). There you can see next point: that you have three missing values for the "receipt qty" and "order qty". May be there you should take care too.
For a QV-newbie an interessting load-script ;-)