The key thing here is how you set the values of cell2 and cell3, and you
didn't post that code which you should have. But based on your description,
you're passing Counta the "value" of the cells rather than the cells
themselves. The value of empty cells is 0 for many purposes (e.g., enter
=A1 in a cell and it returns 0 even though A1 is empty) and 0 is not empty.

These examples illustrate what I think is going on. In both, A1 and A2 are
empty:

Sub Bad()
Dim Cell1Val As Variant
Dim Cell2Val As Variant
Cell1Val = Range("A1").Value
Cell2Val = Range("A2").Value
MsgBox Application.CountA(Cell1Val, Cell2Val) ''2
End Sub

Sub Good()
Dim Cell1Rg As Range
Dim Cell2Rg As Range
Set Cell1Rg = Range("A1")
Set Cell2Rg = Range("A2")
MsgBox Application.CountA(Cell1Rg, Cell2Rg) ''0
End Sub


--
Jim Rech
Excel MVP