There are multiple entry points into
ebay for combining lots on an invoice. The only one that seems to work reliably is to just click "send invoice" on one lot when none of them are paid for. I did this today and it worked fine. It automatically combined the lots for me. The "combine orders" methods has always been buggy.
One hint I use when there are multiple lots that cannot be combined is that you can still use a single mailing label. Just use it for one lot and you can copy/paste the tracking number on the other lots in the package. The buyer will be notified that all the lots have been shipped.
ebay is very very slow at fixing bugs. There's one on printing mailing labels that requires a workaround that I've been using for months. One day they may fix it - but there is no way to report a bug and actually have it tracked.