I have exactly the same problem. I have been working in Evernote for a few hours now and it is consuming 3.55 GB of memory (yes, you read that right). I just restarted it and memory usage is now 172 MB. This is extremely frustrating. Evernote version 6.10 (454267 Direct) OS X El Capitan version 10.11.6 (15G1212)
I am having the same problem. When I attempt to clip a rectangle, what actually gets clipped is offset by about 180px downward, so I have to draw my rectangle about 180px above what I'm actually trying to clip. That works, however sometimes part of the resulting clip is shaded, as if a dark low-transparency rectangle were superimposed over it.