Do you currently log details about the orders that are successful from PayPal? The reason I ask is that in order to determine why some orders would not be saved to the db correctly it would be necessary to compare the details of those orders to the details of the orders that are being stored correctly. Unless it is truly a sporadic issue there should be some pattern to the orders so long as the code is not changing in the mean time.
Unless this was a problem with the server not executing the same code consistently there should be some common element to the orders that are not making it in, perhaps a particular item is present or the amounts are a little different on the bad orders. Any info that you could create or provide that would allow you to compare them would be the first step in attempting to troubleshoot what is going wrong. You can add in your own insert server behavior to record details of orders then compare later to the ones that are stored in the orders table to determine which ones are not getting saved and why.