Update:
Issue still persists, but I noticed something today that is not part of my OP(see items in red below). The issue is on the redirect after clicking the link. "Lemme espain...no there is too much...lemme sum up"...
The "Disk Usage" link on the main Jenkins page links to "http://server.hostname.net/jenkins/disk-usage". After clicking this link you get a redirect that happens and it sends you to "http://server.hostname.net:8080/jenkins/plugins/disk-usage" and it should be "http://server.hostname.net/jenkins/plugins/disk-usage" (No ':8080').
After the redirect if I delete the :8080 part in the address bar the page loads properly. 
So I'm not sure if it's the plugin or the main Jenkins code that is doing the "redirect"; but whomever is handling that part is not obeying the "System configuration>Jenkins URL = http://server.host.net/jenkins/" entry and injecting the ":8080" part.
Also not sure if this is only a problem with the Jenkins/disk-usage when deployed to an app server using the Jenkins.war install method.
Would love to see an update on this issue. Perhaps it's resolved in the "Upcoming 0.29 release" that has yet to be actually released! 
This issue doesn't happen in version 0.25 but starts with version 0.26