Hi Imran,
I am again saying the same thing. There is high possibility that when you invoiced this sales order, there were not enough financial updated purchases. And after sales order invoicing, some purchase orders are also invoiced (financially updated). As a result, now when you are running the recalculation, all the issues (sales/transfers) will be valued at FIFO basis.
To avoid this in future, there is one more option. On inventory model group, there is a check box 'include physical value' at the bottom of the form. You can check that so that every time you issue(sell), inspite of having no financial updated receipts, it considers the physical receipt values.
I hope it will clarify. So, you should really analyse invent trans w.r.t. invent date, physical date and financial date.