It looks like its not even reading the next line of code in the scipt until the "yes" is pushed on the dialog box.

...
...
$ie->getButton('name:', "button1")->Click; ##submits form on previous 
+page

print "made it here"; ## doesnt print until "yes" is clicked on securi
+ty dialog box
...
...
[download]

So its not even making it to the
$clicker->push_security_alert_yes();