There's a pretty serious bug in the new Safari Clipper extension. This is happening on two educational CMS sites, Blackboard, and Blackbaud (yeah, what's with the names?). When these pages load, the Clipper also loads without user prompting. What's worse is that the clipper can't be dismissed when you click the "x." In fact, sometimes new Clipper sub-windows load, overlapping each other, and they can't be dismissed either. On Blackboard pages, they even interfere with the user's ability to interact with the main page content.
Clearly there's some weird code on these sites that's messing with the extension (which doesn't surprise me, as educational CMS developers seem to care very little for established web standards - until recently, Blackbaud still insisted that Internet Explorer was the best browser to use with it, despite the fact that IE on the Mac has been defunct for years).
Hopefully someone at Evernote is monitoring these forums and can have a look at this issue.