Keep in mind you’re using a version of the theme that we no longer support. Almost a year ago, we completely re-did the theme from scratch (which you can download for free from ThemeForest).
I just dug up the last 1.x version of Alyeska and can see why you’re having these odd issues. I’m just sort of speculating by looking back at the old code, but in theory, this should fix your issue.
Open this file: /includes/theme_functions/alyeska_portfolio.php
Find this towards the top:
$query_string = "post_type=portfolio-item&order=ASC&orderby=menu_order&posts_per_page=$num";
And change it to this:
$query_string = "post_type=portfolio-item&posts_per_page=$num";
Now they should be ordered by their publish date.