I've been using Hype as of v3.5 so do not have a reference with other versions to compare~test this issue.
Clicking on these "Plus" elements does not trigger the alert() initially. Upon first opening the Preview, clicking the "1st Panel Plus" element opens (& closes when clicking the "x") the panels like it should - but no alert() was triggered. The other two Plus elements register nothing until You click them a second time (as with your code), which only then shows the "alert" dialog. Curiously, if You first click on the "2nd Panel Plus" and/or "3rd Panel Plus" - then click on "1st Panel Plus" it immediately registers alert(), second click not required.
I've also tried using "mouseDown" instead of "Click~Tap"; clearing out the code in the Header even though it appeared to have nothing to do with the issue at hand; and tried different browsers.
Keeping the "alert()" functions in place, I then removed the initial "Pause" in the timeline (00:00.00) - basically the same result - two clicks required to display an "alert" dialog.
I then solo'd all scenes (deleting the others), each in turn - "Feature Ad", "Second Ad", "Third Ad".
The "Third Ad" scene (solo) was the only time that the buttons registered a click the first time.
Hopefully You might glean something of value from this info. I'm puzzled & clearly missing something... the variety of set-ups would seem to militate against a straightforward bug.