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I actually need this so bad that I do it the ridiculously hard way -- open up the Mac font palette, click on background color button which opens up the color selection palette, then keep both of them open while I read or edit a note. There's a bug in the editor that forces me to keep the font palette open because the color palette sometimes resets to affecting the foreground color. I have to undo each time this happens, click background color again, and then choose a tiny "favorited" square at the bottom of my standard highlight color. I have been using the highlight feature in Clearly and totally love it. The problem with Clearly is that I can't see my highlights again if I close the tab and come back to the page later. If I want to read, say, the first half of a long article, I could highlight as I read, save it to my Evernote account, then continue reading and highlighting there.
I had a very similar issue. Go to "Help -> Activity Log" and look at the log output. There might be something in there about a parse error on a specific note. For me, I had a parse error on a note I created with the iOS app that had only a camera photo in it. I logged into the web interface, deleted the note, deleted it in the Mac app (both by moving it to the trash, then deleting it in the trash) and that fixed it for me.