I just tested this because I thought it happened to me (a new note getting put into the wrong stack), but I think I clicked New Note while evernote was open to a non-inbox stack at the time and that is where my new notes went. If evernote is minimized to the notification area and you right-click and choose new note or use the ctrl-alt n keyboard shortcut the new note is put into the inbox. I'm pretty sure you can also change the default "inbox" stack to be anything you want in the options screen.
