OK, I got it working eventually. I'm not sure if it was configuring the scansnap to scan to mobile or reinstalling Evernote. If anyone is having similar problems I suspect its the latter.
Having done that I went to Scan Snap Home (the app on my PC) I selected LOCAL MODE and configured a new profile for Evernote.
Note, I can no longer get the cloud mode in Scan Snap to work for Evernote. This was the method I had followed up to now based on readily available advice on the internet.