Hi Atlas,
I took a look at this report, and wasn't able to see the same behavior--'At Risk' applications seem to display correctly for me. However, date/time calculation is fairly complicated for determining that something is late/at risk, so it's possible that there's some query that isn't inclusive enough here.
This view should show At Risk applications, as long as they belong to the company that you're selecting on the first screen of the report. Are the missing applications available when you select 'Single Application Request' on this report?