Adding an adminhtml layout update breaks the re-index page here are my xmls.
The third file is an alternative for the layout update with nothing in, which still breaks the index page.
config.xml
<config>
<adminhtml>
<layout>
<updates>
<index>
<file>module/file.xml</file>
</index>
</updates>
</layout>
</adminhtml>
</config>
module/file.xml
<layout>
<default>
<reference name="notifications">
<block type="module/adminhtml_notifications" name="module_notifications" template="company/module/notifications.phtml"/>
</reference>
</default>
</layout>
Still breaks with this: module/file.xml
<layout>
</layout>