I had to work from a Citrix client for a few years, and didn't much care for it. Through a T1 connection services such as browsing a remote filesystem were painfully slow. But that doesn't have anything to do with your question; I'm just sympathizing. :)

On the Citrix server, user account properties, session tab, you can ask the administrator to disable timeout by setting idle timeout to never.

There are also strategies you can use from the client side, which are documented in citrix support article #CTX105717. Google is a wonderful resource: keeping a citrix logon alive.

If those don't work you could always use Windows scheduler to fire up a Perl script that 'tickles' Citrix through the Windows API every hour or so. I'm envisioning a script that gives the impression of Windows user starting up and stopping again some application that involves hitting the Citrix server.