oh my word, I would be livid!! Photos are so important to me (and presumably to all of us who are willing to pay these outrageous prices). I'm so sorry this is happening. I hope they find those photos AND refund your money for the stress and hassle.
On the Magic last month I noticed a few were missing when I looked at the kiosk, and they weren't in with the printed pics in the folio. I spoke to someone (fortunately this was mid-cruise and there was no line), once he finally believed me he called some magical person on the phone, described the time/location of the photos and informed me the pictures would be found and show up in about an hour. Sure enough, when we checked the kiosk that evening they were there, and they were on the CD as well.
I wonder if it's a problem with the USB process? The CD actually doesn't contain the photos, it just has software that downloads them from a website. Does the USB have the actual photo files or software to download?