Technical Info:
Drupal - 5.1
Theme - Barlow
Menu by role - 5.1 version
Applied Patch from readme.txt file

I am a new DRUPAL user, building a site for a non-profit organization. I am using a high level primary menu for non-authenticated users, and a second menu for authenticated users. I have been working for 90 minutes customizing my secondary navigation using the module and I was making good progress. Then I made changes two final changes to my authenticated role menu and found that my primary top level navigation disappeared.

Uninstalling the module and replacing the menu.inc file brought back my primary default navigation.

Comments

Title:Main Navigation (top level) Menu Vanishes for Non-Authenticated usersmenu item for Non-Authenticated users

Possible that they menu has been already disappeared earlier?

It might happen, that a menu item is not visible even if it's not restricted. This happens when multiple menu items are pointing at the same path.
If you have such a menu item in the block, the block won't appear, when them item doesn't appear.

Status:Active» Closed (won't fix)

This is 3 years old... I'm closing it. Hopefully you'll be able to upgrade to 6.x and get that resolved. There are no 5.x maintainers.