We’ve actually had some trouble with PLP and shortcodes in the past so this was a good opportunity to revisit the issue.
In effect, we found the automatic excerpt generated by WordPress was affecting the Auto Pagination module. When we supplied a handmade excerpt, the shortcode didn’t affect pagination. However, if we left the excerpt field blank, allowing WordPress to generate it, the shortcode would break.
We fixed this by adding a filter to the core plugin that will generate an excerpt if users leave the field blank. This should avoid shortcode breakage and will fix other kinds of implementation in which the auto-generated excerpt is used.
We’ll be releasing v.1.2.2 of the Auto Pagination module, and 2.3.2 of Page-Links Plus, in the next day or so.