I find the alert box is a bit much as well. Maybe change the status icon somewhat to signify if it's in sync or not?
I also got a 404 error when I started it the first time. I'm assuming since it didn't find the NeatList directory that it then created. It may confuse / annoy new users into thinking the app doesn't work right, may want to make that a silent check & fix.
You should probably charge something for this app.
Only one nitpick: Remove the alert box that comes after syncing is complete.
Are you going to add any more feature (reminders or due-dates?).