Once your validation get done you have to return false if its wrong,
var regex = /^\d{4}$/;
if (document.ExamEntry.Examination_number.value == "") {
msg+="You must enter your examination number";
result = false;
} else if (isNaN(document.ExamEntry.Examination_number.value)) {
msg+="Examination number should only contain digits";
result = false;
} else if (!regex.test(document.ExamEntry.Examination_number.value)) {
msg+="Examination number should contain exactly 4 digits";
result = false;
}