I've got one weird issue with Evernote for Windows. I'm on version 10.6.9-win-ddl-public (2254).
Whenever I first go into Evernote after a reboot or power on, it always opens to the same note. It's a fairly arbitrary note, but it's always the same one, and has been stuck that way over the last couple of Evernote versions.
If I exit from Evernote and go back in, within the same session (not logging out or rebooting or anything), then it behaves as expected, and returns to the note I was working on last.
I hope I've explained that well. I did a little searching here and didn't find any similar issues.
And I also use Evernote for Mac, and I don't experience this issue there. (Though, come to think of it, I almost never actually reboot or power down my Mac. I usually just put it to sleep.)