It seems that current implementation of UpdateCenter fails to find any plugins that exists in multiple repositories (sites) and is using only the version found on the first repository.

<sites>
<site>
<id>default</id>
<url>http://updates.jenkins-ci.org/stable/update-center.json</url>
</site>
<site>
<id>custom</id>
<url>http://example.com/update-center/jenkins/update-center.json</url>
</site>
</sites>

If default site includes foobar-1.0 and custom site includes foobar-1.2, Jenkins will find only foobar-1.0.

This is critical because due to the lots of dependencies between Jenkins plugins it makes almost impossible to work with multiple sites. At current stage multiple sites works only if you do not have overlapping plugins.