I figured it out. I had to add a listener for the infoWindow's domready event and call my jPages from within there. Working perfectly now.
// Add event listener for the infoWindow
google.maps.event.addListener(cbMapInfoWindow, 'domready', function() {
$('#cboxLoadedContent iframe').contents().find('.infoWindowHolder').jPages({
containerID : "infoWindowContainer"
});
});
JSFiddle