Intercompany invoicing problems

We have been doing intercompany invoicing for cross-charged costs (between operating units) for several years, and have a couple problems that show up frequently.

One is that the invoices coming into AP will randomly 'get the lines mixed up'.  The actual error is something about the header level not matching the line level details, but when you look closely, you can see that lines belonging to one intercompany invoice have been attached to a different one, making the header amount not equal the total of the line amounts.  I opened a SR awhile back, but got too frustrated because this is not repeatable.  I will try again, but wanted to see if anyone else has experienced this first.