PBI Desktop to Service not matching data

Filters and slicer selections are persistent between sessions, regardless of republishing the data. I would look at those. Hover over the Filter icon in the service and see what is filtering that data.  On the desktop it is the old funnel icon.

That still might not tell the whole story as hidden filters do not show up when you hover over it - they are hidden but still affect it. 

Also reset all bookmarks to default - and this will also reset filters using the clockwise circle arrow in the upper right.

This will ensure everything is back to the default of the published report.