ScriptEngine configuration is being ignored

I have a custom application for Adobe Media Server. I am trying to set up the Application.xml file and the config isn't loading properly. This is not working:

<ScriptEngine>
<config>
<createTransferFile>true</createTransferFile>
<maxDVRRollingWindow>-1</maxDVRRollingWindow>
</config>
</ScriptEngine>

This really old config which is supposed to be deprecated seems to work:

<JSEngine>
<ApplicationObject>
<config>
<createTransferFile>true</createTransferFile>
<maxDVRRollingWindow>-1</maxDVRRollingWindow>
</config>
</ApplicationObject>
</JSEngine>

Any suggestions on what is happening? I am also trying to configure FileObject, and it isn't working. I think it may be related to this really strange behavior with the config files.