This doesn't sound familiar. What I think is happening is that ERAS is doling them out that way. In batches I've had candidates tell me that everything is in, but ERAS may not push it all through to us at once. For example, I may get most of your documents in the morning, but your USMLE may not come through to me until the evening or next day along with 100 other USMLE transcripts. It's par for the course.
We've never filtered the downloads and I'm not in front of the workstation right now, so I can't say with 100% certainty right now that it's not possible. But I'll look into it and get back to you. What I know we can control is how and what we print from submissions, but you guys would't have any way to see/know that.
I'll tell you that we've been experiencing some delays and glitches just as you did earlier, so that may add to the hiccups you're seeing.