Previous versions of Fieldable Panels Panes used a preprocess function to generate the FPP object's output, resulting in the template only responsible for outputting a variable; this is contrary to Drupal 7's standard practice of using render arrays at the template level.
Fieldable Panels Panes v7.x-1.6-beta1 introduces a change to this output structure. The preprocess function no longer generates the output HTML, instead the fieldable-panels-pane.tpl.php file uses the standard render() function to generate it.
In previous versions of Fieldable Panels Panes the fieldable-panels-pane.tpl.php file contained the following code:
print $fields;
The fieldable-panels-pane.tpl.php in 1.6-beta1 and newer contain the following:
print render($content);
As a result, any overridden fieldable-panels-pane.tpl.php files will need to be updated to match the new structure.