Never happened to me, at least not when opening the Dropbox folder on my computer from the Dropbox menu bar item.
I have, however, mixed up Dropbox accounts before and then I was wondering why something that I had put into the Dropbox folder on my Mac was not showing up in my (other) Dropbox account on the web. Are you sure that you put the folder into the same Dropbox account which's folder on your Mac is open?