The correct signature for the setTimeout function is as follows:
var timeoutID = window.setTimeout(func, delay, [param1, param2, ...]);
var timeoutID = window.setTimeout(code, delay);
Your second example works because you are actually defining a function within the setTimeout call.
Your first example is actually the second signature here. So for it to work, you'd have to deal with it as if it was code and pass it as a string (similar to eval() ).
setTimeout( "player.stopVideo()", 1000 );
Here is a link to the resource and an excerpt from the description of the parameters:
func is the function you want to execute after delay milliseconds.
code in the alternate syntax is a string of code you want to execute after delay milliseconds (using this syntax is not recommended for the same reasons as using eval())
player.