Just got around to installing it (via 2-step authentication).
Same problem. Mac 10.9.4, Safari 7.0.5, Webclipper 6.1.3 Macbook retina 2013, no other extensions installed!
I will also get the large dotted clock-like face waiting/hourglass icon in the middle of the web page until i reload the page. After I restart Safari sometime it will work on the same web page where it didn't before the restart.
As one software developer to another saying it "works on my machine" is unexceptable.. Set up a share screen session with someone or ask for log dumps, whatever.
My web clipper works fine on my iMac with the same settings, so something subtle is going on and it's probably hardware related.