GOOD NEWS!
Here is the permanent fix for this. The problem IS caused by the plugin Multipage Toolkit (Current version 2.6). The good news is, it can EASILY be fixed. For those interested in the how and why, here it goes:
In the multipage toolkit folder in wp-content/plugins open TA_multi_toolkit.php and observe:
add_action('init', 'allpage_permalink', -1);
function allpage_permalink() {
global $wp_rewrite;
$wp_rewrite->add_endpoint("all", EP_ALL);
$wp_rewrite->flush_rules();
You will find this block of code at line 332. When the plugin is initialized it will flush the rules. For whatever reason, it got away with this on earlier versions of WordPress – beginning with 3.1, this will obliterate certain custom structures (but, interestingly, not all).
The easiest fix if you want to have custom Permalinks AND use Multi-page toolkit is to to remove the line:
$wp_rewrite->flush_rules();
From TA_multi_toolkit.php – the plugin does not need it to function normally.