I have no problem photographing documents with the Evernote app on my iPhone 4S, however, when I sync with my macbook air, sometimes the document will appear in Evernote for mac, as a small rendition of the original size, almost like a thumbnail. The documents are full size on the iphone.
This does not happen with every document, but if its going to happen, it happens every time with that same document. I see nothing peculiar to distinguish the documents that sync properly to those that do not.
I have the latest software on the iphone and mac, which is running Lion 10.7.5.