Have just booked in an order and only the bottom two lines have been booked in. This may be the same problem that VaporPhoxxe has had, I have managed to replicate the situation from a backup. I cant remember if a line item had been removed from the order or anything like that, but the order when save only booked the last lines in and it does not show anything in the B/O field of the lines that had the errors. There were 17 order lines in total, top 15 lines not updated stock, Order is flagged as received, Order lines have a qty figure, B/O says 0, Received says 0.
Whilst I have managed to replicate the error from backup files (I could send them to you if you wish) I have also managed to revert to backup and delete all the line items from the offending purchase order and then add the lines again, this time it updated the stock corrctly. Must be something to do with ammending or changing the purchase order before trying to receive the items.