In Quickbooks Pro Manufacturing Edition are you seeing Purchase Orders on your Open PO report in Quickbooks that have been received in full. Are you seeing the "Received In Full" stamp on these PO's when you open them to try to determine the cause of the error.
Here is a little trick that I have found works well for me. Open the purchase order that is in question (be sure to keep track of the PO number), change the date of the PO to the year 2030 and save and close it. Use the "Find" feature with the PO number or locate it in the Customer center if you no longer see it on the report. Re-open the PO and change the date back to the correct year and save and close it.
Give this a try and please comment on whether or not it has fixed your problem. It has worked well for me and I am curious to find out if others have the same result. Yes, I admit, it's just a treatment and doesn't really diagnose why this is happening.