Previously (1.2 Dev) if you were to put a link into an Assignment activity, when this link was activated it would load the web page and you would still see the Moodle navigation bar in the top portion of the screen. Now (1.2 Beta and +), you are taken outside of Moodle and the linked page loads in a parent window. Is this a change in the feature set for Asssignment module, a problem with the HTML editor, Moodle code or not enough sleep on my part?
Not enough sleep, I think ... 
Last time, did you perhaps link to a Moodle resource that used a framed display?
Last time, did you perhaps link to a Moodle resource that used a framed display?
Ah, sorry. It is in fact not enough sleep. Assignment was a Resource in older site. Guess the old motto, "I'll have plenty of time to sleep when I'm dead," needs revision. 