When creating a recurring invoice, the GL accounts are added in a specific order (line 1, 2, 3, 4 etc). This order should be Static but after the recurring invoice is generated, the order of the GL Accounts are mixed up (3, 2, 4, 1).
It should be expected that these account #s would stay in the same order it was set up. This would make it easier to update the invoice, especially when entering many lines that correspond to a specific order on the invoice. It also makes it easier for the reviewers/people approving.
Attached is a screenshot - on the left is the coding order I set up when creating a recurring template, on the right is the coding order of the generated invoice. The detailed descriptions show how out of order things are. Also note - this invoice normally has 50+ line items. I ended up just deleteing all the account lines in the recurring template and manually enter them each period.