[Plugin: Multi-page Toolkit] Breaks permalinks

ruined my site immediately after upgrade. One user said to go into the plugin and delete the PHP line that has

$wp_rewrite->flush_rules();

But alas, it didnt work for me. I commented out the line, activated the plugin and it breaks again.

*EDIT* ok… it did work. WP was just reacting strangely. Took my two tries disabling the plugin, waiting for it to fix itself (don’t know why it wasnt immediate), and then reactivating with that line commented out.