Try to uninstall it from Safari, quit and restart Safari, re-install the Evernote Web Clipper. That might do the trick. It's what tech support suggested I do and it worked (mind you on Google Chrome).
I'm looking forward to seeing this fixed. I'm a Google Chrome power user and for now I have to keep a Mozilla Firefox browser open for the times I have to web clip something. That is when I want to web clip, I copy the URL page from Chrome, paste in Firefox, then Evernote Web Clip it. There's the work around if you need it.