Custom module Pager does not work with Ajax filter
I have discovered a sort of workaround.  It requires storing the result of current_path() in a JS setting variable, and rewriting the path in JS when the pager is regenerated.

Sample code:

php
// building an ajax form...
global $base_path;
$settings = array(
    'my_module' =&gt; array(
    'my_path' =&gt; $base_path . current_path(),
  ),
);
drupal_add_js($settings, 'setting');


That will make the current page's path available in your JavaScript file to manipulate.  There are still kinks though, especially with AJAX filtering and AJAX paging all at once.  I will update this once I resolve all those kinks.