This is happening to me too. It started as soon as I moved to Sierra (clean install). macOS 10.12.2, Safari 10.0.2 (12602.3.12.0.1), Evernote Web Clipper 6.10.1. Still happens when Evernote Web Clipper is the only extension. Safari preferences/privacy/cookies website data has always been set to "Allow from websites I visit."