I want to point out that whenever we create a goods receipt it create double transaction one with positive qty and other with negative one which i believe is one for Unspecified Location (Default one) and other one with positive qty is for Inventory Location so when you look at Inventory qty on hand by location report Unspecified location shows negative qty. (If there are no inventory location then both positive and negative happens at Unspecified location and you get zero qty on hand on reports.)
Now created Purchase Invoice for the order
Results are fine now after creating invoice.
So in short Inventory Location should be selected on either goods receipt or Invoice to get the correct results.
I think thats the issue most users are complaining about because they select Location on both invoice and Goods receipt.
And one more thing. your results wont be fine until you receive an invoice for the goods you received.
@lubos kindly look into this. Maybe i am missing something.
And the same behaviour is on Selling side. (DNs and sales invoices.)