Not sure if this will be relevent to your situation, but maybe the problem is due to a timezone issue and some items are being flagged as late because they fall outside one day for that reason.

Make sure that your ebay account is registered in the same timezone as you actually reside in.

Also perhaps check to see if the items flagged as late were purchased very early in a day or very late at night.

When I first signed up with ebay many years ago, they registered my account on the US site with an Australian address and AU$ price tags and it wasn't for a few months of things going haywire that we discovered why. I had to get ebay to change it at their end to fix the problems it was causing at the time.

As I said, I don't know whether this suggestion will help you or not but it is something worth looking into.