Microsoft, in an effort to make Internet Explorer 8 "more stable", have changed the underlying architecture of the browser and introduced a function called "Loosely-Coupled IE" (LCIE). 

However, this new function changes the way your users can use the Citrix Java Client to access their applications most importantly, by breaking session sharing.

Fundamentally, with "Loosely-Coupled IE" (LCIE) the IE Team have isolated the browser frame and its tabs and changed them to use asynchronous communication between components. You can read more about the science part here: http://blogs.msdn.com/ie/archive/2008/03/11/ie8-and-loosely-coupled-ie-lcie.aspx
 
While IE8 doesn't prevent access to Citrix Java Client users, it does change the user experience.
 
With previous versions of IE (and other browsers) when you launch an application using the Citrix Java Client, it causes a java session to be started. Your application then runs via the Citrix Java Client in that java session instance. Subsequent applications, launched concurrently, are also launched using the same java session: this means that other applications also run in the same Citrix session using the same Citrix Java Client.

IE8's new  LCIE causes each application launch to be run in an individual java runtime session.

This means that, in turn, each application runs in its own session. Not particularly bad if your users only access one application, they access a published desktop, or applications are explicity hosted on different environments. Yet, if you publish multiple applications (say from the same server) - each application launch will cause the user to go through the logon process again, cause their profile to be loaded again, cause printers to be mapped again, require remote drive mappings to be mapped again.

If you're using the Citrix Java Client its likely you're allowing remote access. It's also likely you've locked down the user's Citrix client functionality for security.

You may have locked down the ability to cut and paste: preventing users from cutting and pasting to the local desktop. Normally, this at least allows users to cut and paste between Citrix applications. LCIE will stop this from working with the Java Client. You may have implemented an 'idle time' for each session. Your idle time (i.e. the time before you are logged off if you've been away from your device) is based on the session idle time. As each application is running in its own session - users will receive prompts of idle time expiry - because while they might be working in one application, the idle time counter for another application (which is running in another session) is counting down.

How can you resolve this?

a) Don't use IE8: other browsers are available. 

b) You can make a registry change on the client PC  - adding the following:

[HKEY_CURRENT_USER\Software\Microsoft\Internet Explorer\Main]
"TabProcGrowth"=dword:00000000

Will disable "Loosely Couple IE8"; IE8 then works as previous versions of IE and Citrix Java Client session sharing is enabled again.

Its unlikely Citrix will update the Java Client to resolve this as its an issue with IE, not the Java Client. Hopefully, Microsoft will at least provide disabling/enabling LCIE an option with the advanced tab of IE.