Running a partial string formatting macro more than once messes up

The issue appears to be occurring on the line

ActiveSheet.Cells(Row, Col2).Value = LCase(ActiveSheet.Cells(Row, Col2).Value)

As you have converted to lower case the first time, you don't need to on subsequent occasions

Try this

If ActiveSheet.Cells(Row, Col2).Value <> LCase(ActiveSheet.Cells(Row, Col2).Value) Then
    ActiveSheet.Cells(Row, Col2).Value = LCase(ActiveSheet.Cells(Row, Col2).Value)
End If