Ok, I found the solution at Jetpack’s website, http://jetpack.me/support/infinite-scroll/
I just needed to insert the custom scrollbar’s update function inside this function provided by jetpack’s infinite scroll.
“JavaScript Events
Inevitably, there are situations in a theme that require some JavaScript interaction after posts are added. One such example is in a theme that uses jQuery Masonry and needs to trigger that library to position the additional posts. Recognizing this need, we trigger an event after posts are appended. To make use of this event, simply catch the post-load event when it fires on document.body:”
( function( $ ) {
$( document.body ).on( 'post-load', function () {
// New posts have been added to the page.
} );
} )( jQuery );
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