use setTimeout

var timeout;
function animate()
{
    // do stuff here
    clearTimeout(timeout);
    timeout=setTimeout(animate,2500);
}

This is an example which settimeout works fine, in fact, it just clear a time before we call it.

and another solution is to do like this:

function test(){
...
    if (....){       
        setTimeout(function(){test();}, 1000);  

    }
}

or ,we can not this more easily:

function test(){
...
    if (....){       
        setTimeout(test, 1000);  

    }
}

further more,

window.setTimeout('window.parent.generateOutput(true)', 1000);  // deprecated

is deprecated. So it explain why it works sometimes for the older version of spoop.

you can see the reference :
https://developer.mozilla.org/en/DOM/window.setTimeout