Ok try this one:
See //Add this
comments
Full Code:
<?php get_header(); ?>
<div class="grid_12 projects">
<?php
if (have_posts()) :
$i = 1; //Add this
while (have_posts()) :
//Add this
if ($i === 1) {
$new_class = "alpha";
}
elseif ($i % 3 == 0) {
$new_class = "omega";
$i = 0;
} else {
$new_class = "";
}
//End
?>
<div class="grid_4 project <?php echo $new_class; ?>">
<!-- ^^^^^^^^^^^^^^^^^^^-->
<?php
the_post();
?>
<a href="<?php the_permalink(); ?>" title="<?php the_title_attribute(); ?>">
<?php the_post_thumbnail(); ?>
</a>
<h2>
<a href="<?php the_permalink(); ?>" title="<?php the_title_attribute(); ?>">
<?php the_title(); ?>
</a>
</h2>
</div><!-- PROJECT ENDS -->
<?php
$i++; //Add this
endwhile;
endif;
?>
</div><!-- PROJECT-CONTAINER ENDS -->
<?php get_footer(); ?>