I do not know if it is still true but when we first started seeing NM, one of the things we had to do to make it work right was to remove almost all pre-existing contents to /etc/network/interfaces and let NM work.  It seems you could add things after it was working right, but I've always done that invoking the "Edit Connections" entry for the right click menu of the NM applet.  I may be way off base here but maybe Lisa can correct me.