copying a range to first empty row is copying over data

Maybe like this (untested):

Sub test3()
    Dim x       As Long
    Dim y       As Long
    Dim wksFr   As Worksheet
    Dim wksTo   As Worksheet

    Set wksFr = Workbooks("Recon Builder.xls").Worksheets("JEs")

    Workbooks.Open Filename:="M:\aaclosing\2008\test\Funding Entries.xls"
    Set wksTo = ActiveWorkbook.Worksheets("Funding Entries")

    x = wksFr.Cells(Rows.Count, "A").End(xlUp).Row
    y = wksTo.Cells(Rows.Count, "A").End(xlUp).Row + 1

    wksFr.Range("A2:G" & x).Copy
    wksTo.Cells(y, "A").PasteSpecial Paste:=xlPasteValues, Operation:=xlNone, _
                                     SkipBlanks:=False, Transpose:=False
End Sub