It sounds like probably this bug report matches what I ran into today (or at least, the later comments do).
I have a New Quizzes assignment that my whole class did, and the New Quizzes Moderate page shows completed attempts for everyone, but for just one student in the class the main gradebook shows "missing" and SpeedGrader shows an empty "no submission" page (with no option to enter a grade anyway: I had to do that manually in the gradebook). For that "missing" student, I was able to use the Moderate page to view their submission and download the attached file, but that workaround isn't great. (I'm lucky I thought to check Moderate at all! Otherwise there was zero indication that the student had completed the assignment.)
I can't find anything that would single out this student from the rest of the class. They had the same deadline as (almost) everyone else, they don't have any unique accommodations, their elapsed time was similar to other students' time, they weren't the first or last one done, they're in the middle of the alphabet... I'm stumped.
A final note/update/solution: jlubkinchavez above shared a workaround involving adding a fudge point, submitting the grade, and taking it away again. It hadn't actually hit me that the individual student attempt entry under Moderate had the grading interface active (it's the left side of the SpeedGrader interface). So I went there, hit the green checkmark for my file upload problem, entered a score, and clicked Update, and now everything is fine (almost): the score shows up in the gradebook, and SpeedGrader shows the student's submission correctly. The only lingering issue is that now the gradebook has marked the submission as "late" (which is better than missing!), even though the student's submission was entirely on time.