The report count on the CMS website references the current set of data CMS has published.  

However, CMS sometimes deletes or overwrite reports, for example next quarter these number may change slightly.  The HFS HCRIS database keeps all reports in the database, so even if later CMS overwrites a report HCRIS keeps both old and new.  Also if CMS deletes a report from a set, the HFS HCRIS database does not delete it.  The HFS HCRIS database keeps the whole history of reports, it’s not “refreshing” the DB based on latest data, rather it’s always and only appending new reports.

CMS may decide to remove a report submitted twice by mistake or exact duplicates while HCRIS keeps everything.