For some reason Microsoft decided to limit the number of sites in the navigation to 50. If you have a large SharePoint organization or have imported from MS-CMS that you will almost certainly break that. But after a lot of bang my head on the wall I call MS
support and got the answer.

In the web.config for the site you are working on, located in C:\Inetpub\wwwroot\wss\VirtualDirectories\(Your port number), find name=GlobalNavSiteMapProfider. From there change the next 8 lines. Add DynamicChildLimit=”75″ to the end of the each one. You can change it it any number you like but 75 was good for me. Setting it to ‘0′ makes it unlimited. Sorry this is not web friendly.

<add name=”GlobalNavSiteMapProvider” description=”CMS provider for Global navigation” type=”Microsoft.SharePoint.Publishing.Navigation.PortalSiteMapProvider, Microsoft.SharePoint.Publishing, Version=12.0.0.0, Culture=neutral, PublicKeyToken=71e9bce111e9429c” NavigationType=”Global” EncodeOutput=”true” DynamicChildLimit=”75″/>

<add name=”CombinedNavSiteMapProvider” description=”CMS provider for Combined navigation” type=”Microsoft.SharePoint.Publishing.Navigation.PortalSiteMapProvider, Microsoft.SharePoint.Publishing, Version=12.0.0.0, Culture=neutral, PublicKeyToken=71e9bce111e9429c” NavigationType=”Combined” EncodeOutput=”true” DynamicChildLimit=”75″ />

<add name=”CurrentNavSiteMapProvider” description=”CMS provider for Current navigation” type=”Microsoft.SharePoint.Publishing.Navigation.PortalSiteMapProvider, Microsoft.SharePoint.Publishing, Version=12.0.0.0, Culture=neutral, PublicKeyToken=71e9bce111e9429c” NavigationType=”Current” EncodeOutput=”true” DynamicChildLimit=”75″ />

<add name=”CurrentNavSiteMapProviderNoEncode” description=”CMS provider for Current navigation, no encoding of output” type=”Microsoft.SharePoint.Publishing.Navigation.PortalSiteMapProvider, Microsoft.SharePoint.Publishing, Version=12.0.0.0, Culture=neutral, PublicKeyToken=71e9bce111e9429c” NavigationType=”Current” EncodeOutput=”false” DynamicChildLimit=”75″ />

<add name=”SiteDirectoryCategoryProvider” description=”Site Directory category provider” type=”Microsoft.SharePoint.Portal.WebControls.SiteDirectoryCategoryProvider, Microsoft.SharePoint.Portal, Version=12.0.0.0, Culture=neutral, PublicKeyToken=71e9bce111e9429c” DynamicChildLimit=”75″ />

<add name=”MySiteMapProvider” description=”MySite provider that returns areas and based on the current user context” type=”Microsoft.SharePoint.Portal.MySiteMapProvider, Microsoft.SharePoint.Portal, Version=12.0.0.0, Culture=neutral, PublicKeyToken=71e9bce111e9429c” DynamicChildLimit=”75″ />

<add name=”MySiteLeftNavProvider” description=”MySite Left Nav provider that returns areas and based on the current user context” type=”Microsoft.SharePoint.Portal.MySiteLeftNavProvider, Microsoft.SharePoint.Portal, Version=12.0.0.0, Culture=neutral, PublicKeyToken=71e9bce111e9429c” DynamicChildLimit=”75″ />

<add name=”UsagePagesSiteMapProvider” description=”Provider for navigation in Portal Usage pages” type=”Microsoft.SharePoint.Portal.Analytics.UsagePagesSiteMapProvider, Microsoft.SharePoint.Portal, Version=12.0.0.0, Culture=neutral, PublicKeyToken=71e9bce111e9429c” DynamicChildLimit=”75″ />