There should be an issue reported in the browser's script console if that happens.

Please also provide the custom JavaScript you're injecting into Jenkins with the Simple Theme plugin.

Of course.
The console on Firefox throws me the error "ReferenceError: RumID is not defined". Also, the CSS that the plugin uses by default appears to be https://ec01c392919812c4f818-79afe539d963810002081e6e2a51e67e.ssl.cf2.rackcdn.com/Embed.js.
However, I am unable to change it, as that would require saving my settings, which will result in a "HTTP ERROR 400" page (attachment 2).

Do you recognize that URL/hostname? Is that your box?

To clarify, when you disable Simple Theme plugin (and nothing else), things magically work again after a Jenkins restart? There were no other updates or anything else?

I'm asking because there is no such thing as a default script for Simple Theme Plugin. In fact, the plugin barely does anything.

The complete source code of the plugin is the following (even if you know nothing about Jenkins' internal API, this will show you how little this plugin does):

• Behavior: Store and retrieve configured URLs for CSS and JS: https://github.com/jenkinsci/simple-theme-plugin/blob/master/src/main/java/org/codefirst/SimpleThemeDecorator.java
• The config form snippet for entering the JS and CSS URLs: https://github.com/jenkinsci/simple-theme-plugin/blob/master/src/main/resources/org/codefirst/SimpleThemeDecorator/global.jelly
• Injecting custom JS/CSS from URLs if defined in global config into every page: https://github.com/jenkinsci/simple-theme-plugin/blob/master/src/main/resources/org/codefirst/SimpleThemeDecorator/header.jelly

>Do you recognize that URL/hostname? Is that your box?
No, I don't recognize the host "ec01c392919812c4f818-79afe539d963810002081e6e2a51e67e.ssl.cf2.rackcdn.com". I would change it, but I have no way to save the settings on the configure page.

>To clarify, when you disable Simple Theme plugin (and nothing else), things magically work again after a Jenkins restart? There were no other updates or anything else?
Correct, once I disable Simple Theme Plugin, things magically work after Jenkins restarts

What's the content of org.codefirst.SimpleThemeDecorator.xml in JENKINS_HOME?

If URLs/paths are defined, please provide the content of the files at those URLs (relative paths are relative from Jenkins URL).

The output of /var/lib/jenkins/org.codefirst.SimpleThemeDecorator.xml is as follows:

<?xml version='1.0' encoding='UTF-8'?>
<org.codefirst.SimpleThemeDecorator plugin="simple-theme-plugin@0.3">
<cssUrl></cssUrl>
<jsUrl>https://ec01c392919812c4f818-79afe539d963810002081e6e2a51e67e.ssl.cf2.rackcdn.com/Embed.js</jsUrl>
</org.codefirst.SimpleThemeDecorator>

Upon reading this, I removed "https://ec01c392919812c4f818-79afe539d963810002081e6e2a51e67e.ssl.cf2.rackcdn.com/Embed.js" from line 4 and was able to save my configuration. Still not sure why that was included by default.

Not a defect, there is no such default.

Either you installed Jenkins from a different source than jenkins-ci.org, that came with plugins and options preinstalled; or you or one of the other admins of your instance added this configuration some time in the past.

I had a similar problem - with the plugin installed and my skinning JavaScript, the "Loading..." never went away. I think it has to do with event handlers, etc. Try this in your Javascript:

function myFunction() {
  // the stuff you want to do.
}
var body = document.getElementsByTagName('body');
if (window.addEventListener) {
  window.addEventListener('load', myFunction, false);
}
else if (window.attachEvent) {
  window.attachEvent('onload', myFunction );
}

Then it works fine. I didn't run into the other issues.