A common mistake you can run into when installing iFilter for SharePoint 2007 is forgetting to replace the value of the key
HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Office
server\12.0\Search\Setup\ContentIndexCommon\Filters\Extension\.pdf`
with the new value for iFilter, for iFilter 9 platform 64 bit and SharePoint 2007 the value to set is
{E8978DA6-047F-4E3D-9C78-CDBE46041603}
Another error or problem is that the PDFFilter.dll DLL is not registered correctly.
in which case a check can be performed and the problem rectified using regedt32.exe.