I had a similar issue with one school with GRE scores not showing up and also a letter of rec at another. However, I just kept emailing the coordinators and calling the school concerned that they weren't registering on my end, and eventually, they miraculously registered as there for reasons I don't think anyone ever identified. One coordinator even emailed me personally in a new email later to say that the problem is now resolved and my application was complete and it would be reviewed shortly, because she remembered me from my concerned interactions before.
My thinking was I figured at least if there was a log of my actively trying to figure it out and they remembered who I am, then maybe it would count for something in terms of the deadline, or at least couldn't hurt. I didn't let the POI know at one school because it was clear that he sent a generic email to every applicant that emailed him so I assumed he didn't want to be bothered because he did this generic email. At the other school, I had a phone interview before I submitted my application at all, so I did email that POI about the problem as she had previously stated to contact her with any questions or concerns and indicated she was open to more contact with me throughout the process. I'd say to go by the personality of the POIs and what you can determine about how involved they want to be with you at this stage. Some don't want to be at all, and others do--it's just a matter of reading their personality on an individual case basis.
I feel that as long as you are not being ridiculous or impolite about it, it's okay to contact the coordinators as much as necessary to make sure things are complete.