To reproduce the problem:

Have a navigator web application setup to use a sources file:

web.xml fragment:
<context-param>
    <param-name>source_config</param-name>
    <param-value>/path/to/sources.xml</param-value>
</context-param>

Then create a jsp file with:
<%@page import="net.ontopia.topicmaps.entry.TopicMaps"%>
<%@page import="net.ontopia.topicmaps.entry.TopicMapRepositoryIF"%>
<%@page import="net.ontopia.topicmaps.nav2.utils.NavigatorUtils"%>
<%
    TopicMapRepositoryIF navrepo = NavigatorUtils.getNavigatorApplication(pageContext).getTopicMapRepository();
    TopicMapRepositoryIF tmrepo = TopicMaps.getRepository("file:///apps/conf/sources/bedrijfsvoering/bedrijfsvoering-sources.xml");
%>
Navigator provided repository: #<%= navrepo.hashCode() %> = <%= 
navrepo.toString() %><br/>
TopicMaps provided repository: #<%= tmrepo.hashCode() %> = <%= 
tmrepo.toString() %><br/>

Output:
Navigator provided repository: #359728309 = 
net.ontopia.topicmaps.entry.TopicMapSourceManager@157104b5
TopicMaps provided repository: #974993029 = 
net.ontopia.topicmaps.entry.TopicMapSourceManager@3a1d3685

This is caused by the NavigatorApplication because it does not use the 
TopicMaps class's repository map.