I have been seeing this behavior for a while now. I have a standard ubuntu installation using the official package. Every time I reboot the jenkins process to update a plugin of a version my Views and Slave Port configuration are overridden.

For instance my original config.xml includes the following.

views>
<hudson.model.AllView>
<owner class="hudson" reference="../../.."/>
<name>All</name>
<filterExecutors>false</filterExecutors>
<filterQueue>false</filterQueue>
<properties class="hudson.model.View$PropertyList"/>
</hudson.model.AllView>
<listView>
<owner class="hudson" reference="../../.."/>
<name>iOS</name>
<filterExecutors>false</filterExecutors>
<filterQueue>false</filterQueue>
<properties class="hudson.model.View$PropertyList"/>
<jobNames>
<comparator class="hudson.util.CaseInsensitiveComparator"/>
</jobNames>
<jobFilters/>
<columns>
<hudson.views.StatusColumn/>
<hudson.views.WeatherColumn/>
<hudson.views.JobColumn/>
<hudson.views.LastSuccessColumn/>
<hudson.views.LastFailureColumn/>
<hudson.views.LastDurationColumn/>
<hudson.views.BuildButtonColumn/>
</columns>
<includeRegex>(?i).IOS-.</includeRegex>
<recurse>false</recurse>
</listView>
</views>
<primaryView>All</primaryView>
<slaveAgentPort>8098</slaveAgentPort>

After a restart that section of the config.xml is reduced to.
<views>
<hudson.model.AllView>
<owner class="hudson" reference="../../.."/>
<name>All</name>
<filterExecutors>false</filterExecutors>
<filterQueue>false</filterQueue>
<properties class="hudson.model.View$PropertyList"/>
</hudson.model.AllView>
</views>
<primaryView>All</primaryView>
<slaveAgentPort>0</slaveAgentPort>

I have watched the jenkins.log file closely and seen no errors or warnings in regard to why these two things specifically are being reset. What is also strange is that the rest of the core config is persisted and remains unchanged.