I posted the reason behind this problem a couple of days ago, but it doesn't seem to have made it to the forum.
The app store version of Evernote is sandboxed. As such, it can only access files in certain folders. I and others have the same problem with Scansnap software. If you use their "scan to Evernote" function, you have to make sure the scan goes to folders like Documents or Pictures, otherwise it won't work. If you look in the console log when you attempt to save a file to Evernote via this workflow, you'll see sandbox errors. You can verify this by creating a note from a file in, say, the Documents folder. That will work. But try a file from, say, Dropbox, and it won't.
I think the only solution is to use the downloadable version of Evernote rather then the app store version. Not sure of the process to revert to that yet. But then you'll also get back the "print PDF to Evernote" function, which is good!