I have tried similar issue and works fine, try it. It can handle different orientations between PDFs.
// array to hold list of PDF files to be merged
$files = array("a.pdf", "b.pdf", "c.pdf");
$pageCount = 0;
// initiate FPDI
$pdf = new FPDI();
// iterate through the files
foreach ($files AS $file) {
// get the page count
$pageCount = $pdf->setSourceFile($file);
// iterate through all pages
for ($pageNo = 1; $pageNo <= $pageCount; $pageNo++) {
// import a page
$templateId = $pdf->importPage($pageNo);
// get the size of the imported page
$size = $pdf->getTemplateSize($templateId);
// create a page (landscape or portrait depending on the imported page size)
if ($size['w'] > $size['h']) {
$pdf->AddPage('L', array($size['w'], $size['h']));
} else {
$pdf->AddPage('P', array($size['w'], $size['h']));
}
// use the imported page
$pdf->useTemplate($templateId);
$pdf->SetFont('Helvetica');
$pdf->SetXY(5, 5);
$pdf->Write(8, 'Generated by FPDI');
}
}