Do you have a link to your blog with enabled plugin?
Custom fields require some special considerations because they often are not part of the post content itself. You have to mark the area in a template file which part is your content. This can include custom fields.
Please read the installation part of the plugin. There is the part "Custom Fields Support". Look at http://wordpress.org/extend/plugins/pdf24-post-to-pdf/installation/ and also look at the FAQ section http://wordpress.org/extend/plugins/pdf24-post-to-pdf/faq/ which contains some more information about custom fields support.
Generally custom fields must be enclosed by codes so that pdf24 knows which parts to add to the PDF file. This is done by the following code:
<?php pdf24Plugin_begin(); ?>
<?php the_content(); ?>
... Your custom fields code ...
<?php pdf24Plugin_end(); ?>
<?php pdf24Plugin_post(); ?>