Custom Field Type is missing in Feeds Importer

You might need to create a target for your custom field type with the help of hook_feeds_processor_targets_alter and here is a code sample for doing so:

<?php
function MYMODULE_feeds_processor_targets_alter(&$targets, $entity_type, $bundle_name)
{
    foreach (field_info_instances($entity_type, $bundle_name) as $name => $instance)
    {
        $info = field_info_field($name);
        unset($callback);
        if ($info['type']=='MYFIELDTYPE1')
        {
            //The callback for this field type goes here.
            $callback = 'TARGET_SETTER_FOR_MYFIELDTYPE1';
        }

        if ($info['type']=='MYFIELDTYPE2')
        {
            //The callback for this field type goes here.
            $callback = 'TARGET_SETTER_FOR_MYFIELDTYPE2';
        }
        //Add cases for each field type here
        //...

        if (isset($callback))
        {
            $targets[$name] =array(
                'name'=>check_plain($instance['label']),
                'callback' => $callback,
                'description' => t('The @label field of the node.', array('@label' => $instance['label'])),
            );
        }
    }
}
?>