It looks like a bug they fixed in the site tools, but it isn't released yet.
I got my site working properly using a "snapshots" profile just for the site
goal:
<profile>
<id>snapshots</id>
<pluginRepositories>
<pluginRepository>
<id>apache-snapshots</id>
<url>http://people.apache.org/maven-snapshot-repository</url>
</pluginRepository>
</pluginRepositories>
<build>
<pluginManagement>
<plugins>
<!-- This seems to work better
than the default (2008/03/19) because
links on sub-module sites are not broken -->
<plugin>
<artifactId>maven-site-plugin</artifactId>
<version>2.0-beta-7-SNAPSHOT</version>
</plugin>
</plugins>
</pluginManagement>
</build>
</profile>
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