Just updated and PageNavi still works well.

Try these steps, I hope it helps.
1. Deactivate and uninstall your whatever pagination plugin.
2. Deactivate YARPP if you have that plugin installed then Install "Clean Options" plugin, this plugin works like a registry cleaner in Windows... just follow the instruction carefully to clean the orphaned options.
4. Activate YARPP
5. Install and activate WP PageNavi.