A new student will show in the form registers due to the form entered on their student profile, but you also need to add then to each assessment class in order to display in a STEPS class markbook. To check this, go to Admin > Classes > Add Students to Class.
Select the Year and Form they are in. Scroll down looking for a student(s) not assigned to a class. This is the likely reason that they are missing.
Once you locate them, place a tick against their name and the class(es) they should be a member of (e.g. in the example above 1 SLO REA, WRI and MAT). Then click on Save Classes at the base of the page.