Pretty much as Bill said.
If you are looking at JTAlert to see DXCC worked, etc then:
Perhaps you did not click SAVE on the JTAlert screen where you selected Scan and Rebuild Log after Applying to your log.
I have always first selected Sync LOTW QSOs & QSLs on the QSL screen of DXKeeper before running SCAN & REBUILD in JTAlert.
Otherwise JTAlert will not pick up the updated log status.
If the states you have worked are already in DXKeeper then the Scan & Rebuild should pick them up after you have synced with LOTW.
73 Walt - W6SA
You MUST select SAVE to have this applied to JTAlert after the Scan & Rebuild otherwise it does not update the JTAlert stats.