It seems like the order of SetX() and SetY() does matter. As you can see, the second cell-box in the example is located at following coordinates: X:10.00125/Y:80. Actually it should be at x=80. Setting Y-coordinate first fixes the problem. Is it a bug? PHP version used is 5.3.28.
<?php
require('./fpdf/fpdf.php');
$pdf = new FPDF();
$pdf->AddPage();
$pdf->SetFont('Arial','B',16);
$pdf->SetY(50);
$pdf->SetX(80);
$pdf->Cell(0,5,'Coordinates: X:'.$pdf->GetX().'/Y:'.$pdf->GetY(), 1);
$pdf->SetX(80);
$pdf->SetY(80);
$pdf->Cell(0,5,'Coordinates: X:'.$pdf->GetX().'/Y:'.$pdf->GetY(), 1);
$pdf->Output();
?>