The application per computer report and applications per computer and per user reports can be very large and can result in 100s of lines of data.  For this reason, when first loaded it will show the data for only 20 computers.

If you filter these reports using the headings on the report you will be filtering on the 20 displayed computers and not the entire computer estate.  This results in only a few results displaying. 

To display all computer information use the criteria and groups at the top of the page rather than using the headings.  This will start a fresh query against all computers.

Please note with filters specifying a wider range of criteria the page can take a longer time to load.