I'm having the same problem as those above. And it's now 2 years past the most recent post - and STILL an issue. Not good!!!
I'm using Safari on a Mac. Evernote Web Clipper ***** up somehow. When it works Clipper improves my productivity tremendously - when it doesn't UGGGGG - it's painful. It works fine on everything except Disqus Comments. Seems so crazy. Will copy on article from webpage, but not the Disqus comments from that same page.
Sure hope there's a remedy!