This happens when the One-JAR version 0.97.
javax.xml.parsers.DocumentBuilder's parse cannot handle One-Jar-URLs. This came up in a situation when I was using Hadoop from within a One-JAR. The Hadoop Configuration system reads the default XML-configuration files from the library-jars. But the One-JAR Class-loader yields "jar:file://path/to/my/one-jar.jar!/lib/hadoop-core-version.jar!/core-default.xml". This does not seem to be a valid systemId for the used org.xml.sax.InputSource.
In the earlier version of One-JAR (0.96) this did not happen.