In enrol/yui/notification/notification.js under the centerDialogue function, the top and left values of the dialogue box are calculated based upon the bounding box for the page.

However, these don't take into account that the dialogue could be larger than the window (e.g. if you have a very small window size set for some reason).
If this is the case, then the dialogue disappears off the top of the screen.

I suggest setting a minimum top/left of around 15px