WordPress 3.5 custom media upload for your theme options

Your going about it in a way that was unintended. Your javascript code should probably look something like this:

$('.custom_media_upload').click(function(e) {
    e.preventDefault();

    var custom_uploader = wp.media({
        title: 'Custom Title',
        button: {
            text: 'Custom Button Text'
        },
        multiple: false  // Set this to true to allow multiple files to be selected
    })
    .on('select', function() {
        var attachment = custom_uploader.state().get('selection').first().toJSON();
        $('.custom_media_image').attr('src', attachment.url);
        $('.custom_media_url').val(attachment.url);
        $('.custom_media_id').val(attachment.id);
    })
    .open();
});