I too am seeing this. I am using this in Maven like so (the version is 3.0_02-jdk1.5):
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-javadoc-plugin</artifactId>
<version>2.9.1</version>
<configuration>
<!-- Doclet -->
<doclet>ydoc.doclets.YStandard</doclet>
<docletPath>${yworks.uml.path}/lib/ydoc.jar:${yworks.uml.path}/lib/class2svg.jar:${yworks.uml.path}/resources</docletPath>
<additionalparam>-umlautogen</additionalparam>
<!-- bootclasspath required by Sun's JVM -->
<bootclasspath>${sun.boot.class.path}</bootclasspath>
<!-- General Javadoc settings -->
<doctitle>${project.name} (${project.version})</doctitle>
<show>private</show>
<docfilessubdirs>true</docfilessubdirs>
<additionalJOption>-J-Xmx1024m</additionalJOption>
<verbose>true</verbose>
</configuration>
</plugin>
and other than the broken images it seems to work pretty well.