I have had the same problem, the check box in the settings is broken.. I used this: http://answers.microsoft.com/en-us/windows/forum/windows_7-performance/how-to-disable-an-auto-start-program-within/3469b847-5174-4fa5-8918-6ddcabb2426b?db=5&auth=1 removing ever note from startup folders
What would be great is that I write an idea down on a post it note, come back and find that indeed that note hasn't spontaneously disappeared. This would be great if only from a cognitive perspective. Even a sync button on the evernote web ui would again cognitively be copacetic. Alas. No. And yet there is a request of how much $$ to maintain these notes in the cloud, a feat capable pre win 95 on a 54k dialup modem.