I've seen simlar flashing (though not a complete open/close of the pop) and, at least in my case, it's very random. Click the pop ten times and sometimes it'll flash and others not.
Sorry, not really an answer for you.
What Operating System are you using and what Version of FileMaker? Typically I've seen flashing issues mostly on Windows platforms. Anyway, give us some more info.
I have seen this sort of effect when a script trigger is applied, so as you mention that too I assume the culprit lies in there somewhere. I haven't analysed it, just scrapped the trigger.