Its a problem that comes up time and again. It all began when ebay first brought in simple delivery for private sellers. It resulted in broken combined invoices across the board, including businesses. It got so bad I received a heap of negative feedbacks because of it. It then seemed to correct itself months later. Just double check you allow combined invoices in your settings and refresh it, it may help. Its one of the things I did when it happened. I don’t know if it fixed the issue or if it was a technical glitch.
I don’t know if I have this issue currently as Ive not sold anything never mind combine an order. I have auctions ending later so I will be able to take a look then.