You may of come across this behaviour with navigation or the Table of Contents WebPart. These webparts use a Portal Site Map Provider for their datasource. By default these have limits for the dynamic and static navigation behaviour. You can override these by specifying
StaticChildLimit="<int>"
DynamicChildLimit="<int>"
0 represents no limit, whereas 100 states there can be 100 children.
For example:
<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" StaticChildLimit="0" DynamicChildLimit="0" />
<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" StaticChildLimit="0" DynamicChildLimit="0" />
The web.config is usually found in c:\inetpub\wwwroot\wss\VirtualDirectories\sitename\. You can also find this by opening IIS Manager > Expand "Web Sites" > Right click and select properties > select the "Home Directory" tab > look at the local path. Make sure you backup the web.config by making a copy before you make any changes.