iProcurement - stores for internal and external items

We are currently implementing a change for one of our clients, and are separating their iProc stores so that they have one for their internal items (inventory) and one for the external items (bpa's).  When testing the set up, I have been able to search successfully for internal and external items, getting the correct results each time.  We have now moved the change into the clients UAT environment for them to test, and the search results are reacting differently to what they do in our test environments.  For some items, the internal items are being returned when using the external