You may notice a small checkbox floating down near the 'ok' button.. please dont adjust your sets, this is completely normal.
If it is ticked, and you have cow minimised, then, and only then, will cow popup when something happens and your not watching.
If you dont bother ticking the checkbox then stuff will happen in your minimised cow without you being any-the-wiser.
Thankyou superblah for suggesting this natty little feature.. I hope everyone enjoys it.
And for all you keen on scripting, may I draw your attention to read the scripting introduction