That is very poor on ebay's part, they must have the technology to deal with this and they have let you down. You must have been very disappointed.

It shouldn't matter if it is over 90 days, an ebay rep should be able to fix things if they can clearly see a mistake has been made.

I guess the only thing you can take from this experience is if you ever do the right  thing and eg cancel an order for a customer or initiate a refund, that you check out your ratings soon afterwards, just in case.