hi Marian,
can't say whats happening without looking at your initialization
code however
can you take a look at the initSchema() method in [1].
Having said this I have faced an issue with JarLdifSchemaLoader
when used in a servlet container, but
when used LdifSchemaLoader the problem was solved.
Would be great if you provide more info about the environment and
if possible the way you are
initializing the server.
[1]
http://svn.apache.org/viewvc/directory/apacheds/trunk/core-annotations/src/main/java/org/apache/directory/server/core/factory/DefaultDirectoryServiceFactory.java?view=markup
HTH
Kiran Ayyagari