Hi Rscharfer,
As the alert dialog box for HTML5 captivate is not modal, the javascript will not pause after executing the first alert, hence what is happening in your case is that all the three alerts are printed one by one over each other and you are just able to see the last one. when you click on the last one the click goes to all the alerts and closes them all.
try this one, put this script on javascript execute action on a button.
setTimeout(function(){alert('Hello')},300);
setTimeout(function(){alert('Shriyansh')},10000);
setTimeout(function(){alert('Agnihotri')},30000);
The above script will prove you that all the three are executed and you will get all the 3 alert boxes one after other with intervals as 300ms,10secs and 30 secs.
Let me know if there are queries on this.
Thanks and Regards
Shriyansh
Adobe Engineering Team.