Sorry, I didn't explain my problem very well.
I have a published app called BBJ that requires you to log into the Windows domain, so its not anonymous. After you enter your credentials, it opens up the application. If you quit the application, the session remains active on the server. If you log back into the app, it won't ask for your credentials because you already have a session open, so it just brings you right in. Everytime you log in afterwards, it opens a new session, but they get killed as they should when you quit the app. The first session remains active until you terminate it from the CMC. When you log into BBJ, it actually launches a process on a Linux server. When you exit the application, the process on the Linux server terminates, but the Citrix session remains active.
This problem is only happening with this one particular application (BBJ). If I set up Internet Explorer as a published app (for example), the session terminates when you close the app as it should.
This probably doesn't matter, but we just upgraded to FR3/SP3 after I initially posted this.
Thanks,
Chris