I had the same problem and could solve it:
1. Uninstall the old Evernote Scansnap software.
2. Then connect your Scanner to your Mac via USB.
3. You have to change to Scansnap edition here: http://scansnap.fujitsu.com/global/evernote/index.html
4. After the that, it is a piece of cake. Just download the ScanSnap Home and follow the instructions.
Cheers.