There appears to be a few glitches in the invoicing system last night and today.  I tried to make payment for a combined invoice and had a whole lot of unusual problems.

Hopefully they are temporary and just ebay Friday maintenance.

My suggestion would be to mark all items as paid, then unmark as paid, then hopefully they will combine, I have had success with this in the past.

Otherwise, there are also seller settings, I think they are in the area where you set postage rules where you can nominate X amount of days for invoices to be combined,  a longshot, but you might have them set to less than 4 ??