With 100 users in 4 timezones, most of our access is through the corporate portal; Sun One Portal. This is a proxying server that modifies incoming HTML. Version 2.6.1 was working fine except for date popups, but with our change to 3.1.1, the portal has completely mangled the Jira user interface because globals.css is missing.

The problem is in the way the portal server rewites things. It doesn't understand your new <style> tag:

We have patched our instance of Jira 3.1.1 (see attached), but hope you don't make all your style sheet references work this way.

More details;
This works:
<link type="text/css" rel="StyleSheet" href="<%= request.getContextPath() %>/styles/global.css" />
it gets rewritten. Here's what you see when you "view source" from your browser:
<link type="text/css" rel="StyleSheet" href="https://someexternalportal.com/http://test.someinternalserver.com/jira/styles/global.css"/>

This doesn't work:
<style type="text/css" media="screen">@import "<%= request.getContextPath() %>/styles/global.css";</style>
it doesn't get rewritten at all. This is what you see when you do "view source" from your browser:
<link type="text/css" rel="StyleSheet" href="/jira/styles/global.css" />