Indentions in the document are hard to pick up by scanners since they usually don't change the color or shading of a document very much. Better scanners will pick them up, others will not. Photos of the document, however, clearly pick it up.
Only fact check purports to have seen the paper document, upon which the raised seal has magically appeared, (after people noted it's absence). They purported to have photographed the document, but the photos show very poor, maybe deliberately poor, composition, lighting, and so forth.
That's pure bull. The photos look fine to me. I'll let any lurkers judge for themselves:
http://www.factcheck.org/elections-2008/born_in_the_usa.html
Funny then that they show up fine in other Certifications of Live Birth posted on the 'net. Such as this one:
Or this certified copy of a Certificate of Live Birth (it's a little hard to see on this one, but it's there in the upper right, starting near block 7c.