I don't know about you, but when I submitted everything, there was ~10-hour lag between my USMLE transcripts and everything else being uploaded to the post office (USMLE transcripts being uploaded later...a friend of mine still doesn't have his USMLE uploaded for some reason). As a result, a few programs have everything downloaded except my USMLE transcripts. All other programs had logged in and downloaded everything, then logged in again later and downloaded my USMLE once it became available. I'm assuming the few programs that didn't get my USMLE the first time around simply haven't logged in again for a subsequent download.
Not sure how accurate this is, but I saw on another thread that when a program logs on, everything from everyone applying to that program is downloaded to their database automatically...so it's not like they're selectively avoiding you because they didn't get your USMLE the first time around.