No idea I'm afraid, but it's been happening to me too, twice now with Tracked Packet. Expedited and Xpresspost haven't been a problem.
However, a related issue I noticed the other day is that the "shipped" icon did not show up on my Sold Items list next to an item for which I processed a Light Packet label. Now I do realize that the confirmation # itself isn't uploaded for Light/Small Packet, but I'm sure that the "shipped" icon was always uploaded to the item.
In another rather weird situation that may or may not be related to the above, a buyer purchased one item, paid for it (including full shipping), then purchased 3 additional items. I decided to give her a break on the shipping when I sent the invoice, and refunded over 50% of the shipping she paid on the initial item. Four days later, I noticed on my Summary page that it indicated one item was still awaiting payment -- what!? Sure enough, somehow the item I had partially refunded was now showing as unpaid on my "Sold Items" list. I can only hope the buyer wasn't getting annoying reminders for payment!
In all of the above instances I had to input the information manually. Now I am double-checking every sold item to be sure the details are there once I've processed and shipped them.
As usual, I suspect things are going on in the background that are causing glitches like this. Nothing to be done but to be vigilant. I just wish eBay would stop all new changes and concentrate for a few weeks on making the site consistently reliable.