Only a part of array is stored in transient – what could be causing this?

You are using get_the_id() template tag without proper loop.

Your code should be something like this 

<?php
// Get any existing copy of our transient data
$suggest = get_transient('suggest');
if ( false === ( $suggest = get_transient( 'suggest' ) ) ) {
        // It wasn't there, so regenerate the data and save the transient
        $suggest = array();
        // We will loop a custom post type and fetch custom meta from each post to be added into the autosuggest array
        $query = new WP_Query( array( 'post_type' => 'my_custom_post_type', 'posts_per_page' => -1, ) );
        $posts = $query->posts;
            foreach($posts as $the_post) {
                $value1 = get_post_meta( $the_post->ID , '_town', true );
                $value2 = get_post_meta( $the_post->ID , '_quarteroftown', true );
                $value3 = get_post_meta( $the_post->ID , '_street_name', true );
                $value4 = get_post_meta( $the_post->ID , '_supplier_postcode', true );

                if (!in_array($value1, $suggest))
                    {
                        $suggest[] = $value1; 
                    }
                if (!in_array($value2, $suggest))
                    {
                        $suggest[] = $value2; 
                    }
                if (!in_array($value3, $suggest))
                    {
                        $suggest[] = $value3; 
                    }
                if (!in_array($value4, $suggest))
                    {
                        $suggest[] = $value4; 
                    }
                }
        set_transient( 'suggest', $suggest, HOUR_IN_SECONDS );
}; ?>

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