Jean,

You can set a variable called userInteraction and initialize it to 0. When 
user clicks to go to next page, set userInteraction to 1 then go to next 
page. Then edit the custom event for next page to only execute when 
userInteraction is 0.

Like this: 
if (userInteraction == 0) {
  setTimeout(nextPage, 2000);
}

function nextPage() {
  document.getElementById('pagedeck').goToNextPage();
}

Add the event to the button that user would click with custom action:
userInteraction = 1;
gwd.actions.gwdPagedeck.goToPage('pagedeck', 'page1_1', 'none', 1000, 
'linear', 'top');

To set userInteraction to 0, switch to code view, find window.gwd = 
window.gwd || {};
and add this right below it
var userInteraction = 0;

Attached is the file.

San
Google Web Designer team