I know this is a little bit of thread necromancy, but I believe I found a working solution to this issue.
Using Revo Uninstaller, do an advanced uninstall of Evernote, be sure to delete all keys in the registry (I believe there were four keys in mine that I ended up deleting). Be sure you create a system restore point, unless you're like me and you like to live dangerously.
After the program has been completely removed, restart your computer, and install the latest version of Evernote. I got the popup again at this point, but I was able to 'complete' the 5 tasks, including the syncing task. Since then, I haven't had to deal with this *incredibly irritating* bug.
I hope this helps anyone facing this issue.