After a lot of work on this, I think I've worked things out.
The later bug I described occurs when transition is set to zero. If it is set to one or higher links are clickable after the intro dissapears.
A usability suggestion: You could also consider making the "set to zero to turn off" note more clear as to what it does. I assumed it would turn off the entire intro feature. The confusion in part comes because the toggle for turning off the feature is found in an entirely different section/menu.
One item that still seems to be a bug (though it's not nearly as critical) is that if an intro text is entered, but an image is not, the "hide after waiting" element does not seem to work at all.