There seems to be an issue with activating pop-up when a presentation is viewed using ...presentation.html. If a title is given to the slide, pop-ups do not occur when clicking features that are within the area at the top of the slide down to below the vertical area occupied by the slide. This occurs for the entire horizontal space in this area, regardless of the position of the title. This does not occur when maps are viewed with Explorer Online.
It seems that this could be remedied so that only features beneath the title have pop-ups deactivated or none are deactivated within the view area by having the <div than contains the title grab the on-click event.
Yes, you are correct. Currently the div spans the full width of the page and the click doesn't get passed to the map. I'll write up an enhancement request.