var loopingInterval;
var mySlideDeck = jQuery('.slidedeck').slidedeck();
mySlideDeck.vertical();
var interval = 1000;
var firstDelay = 3000;


// initialize an autoplay switch
var autoPlay = false;
var autoPlayLoop = true;

function autoPlayAdvanceLoop(){
	if(autoPlay){
		// Check to see if the current slide is the last slide
		if(mySlideDeck.current == mySlideDeck.slides.length && autoPlayLoop == true){
			// This is the last slide, go to the first slide
			mySlideDeck.goTo(1);
		} else {
			// This is not the last slide, go to the next slide
			mySlideDeck.next();
		}
	}
}

// sets an initial delay
setTimeout(function(){
	loopingInterval = setInterval(autoPlayAdvanceLoop,interval);	// Run the autoPlayAdvanceLoop() function every interval milliseconds
}, firstDelay - interval)
	
autoPlay = true;

// Stop autoPlay if the deck is clicked.
jQuery('.slidedeck').click(function(){
	autoPlay = false;
	clearInterval(loopingInterval);
});

var loopingInterval;
var mySlideDeck = jQuery('.slidedeck').slidedeck();
mySlideDeck.vertical();
var interval = 1000;
var firstDelay = 3000;


// initialize an autoplay switch
var autoPlay = false;
var autoPlayLoop = true;

function autoPlayAdvanceLoop(){
	if(autoPlay){
		// Check to see if the current slide is the last slide
		if(mySlideDeck.current == mySlideDeck.slides.length && autoPlayLoop == true){
			// This is the last slide, go to the first slide
			mySlideDeck.goTo(1);
		} else {
			// This is not the last slide, go to the next slide
			mySlideDeck.next();
		}
	}
}

// sets an initial delay
setTimeout(function(){
	loopingInterval = setInterval(autoPlayAdvanceLoop,interval);	// Run the autoPlayAdvanceLoop() function every interval miliseconds
}, firstDelay - interval)
	
autoPlay = true;

// Stop autoPlay if the deck is clicked.
jQuery('.slidedeck').click(function(){
	autoPlay = false;
	clearInterval(loopingInterval);
});

http://getsatisfaction.com/slidedeck/topics/slide_time

SlideDeck AutoPlay Functionality with First Slide Delay

JavaScript