We need some clarification, since we're not sure what you mean by 'active'. PackageBoot.xml is not editable from the Packages 'view' but can be edited from within the package.
Have you downloaded the content?
Are you able to edit the PackageBoot.xml within the package editor?
If PackageBoot.xml is not editable from within the package editor, then we'd like to schedule some time to look at it with you. Please email your availability to email@example.com/customerportal
Solution was to reinstall the latest service pack for eminentware on the emientware server and import the packages again from the eminentware server. I was importing them from a remote console and it seemed to do the trick importing the packages from the Eminentware server instead of the remote console.
Now, back to patching.
Thanks for all the help Tonya.