I have been having issues with Evernote since before I upgraded to Lion. I use Safari (latest update) and when I click on "Click rectangle or window to Evernote..." the crosshairs start and keep jamming within a nanosecond. This was happening before Lion. Very frustrating. I finally figured out tonight that I can Command+Shift+4 and then select the area to capture. I then dump that screen capture into a new Evernote and it works like a charm. Hopefully, everything will get fixed and back to normal soon, but for now at least I can use it. Love Evernote!