I'm not sure where the problem came from but upon upgrading to Drupal 4.5 my site kept throwing errors here and there. It was trying to do an insert into the Menu table to create the custom menus. But the table wasn't configured properly.

  pid int(10) unsigned NOT NULL default &#039;0&#039;,<br />
  path varchar(255) NOT NULL default &#039;&#039;,<br />
  title varchar(255) NOT NULL default &#039;&#039;,<br />

These three fields were missing from the menu table. After they were added it seems very happy and all is well.