When you log in to the Citrix desktop, you are actually logging on to one of several servers that make up the CSU Citrix environment. Each time you log in (and use EndNote), you may be logged onto a different server.
If you make profile changes such as creating custom fields, you have to export the .XML file with those changes to your own device. Then in your next session of Endnote via Citrix, go to ‘Edit’ > ‘Preferences’ > ‘Reference Types’ and importing the .XML file after opening the library. This has to be done for each session.
Essentially the profile you save on one session of EndNote won't be there on subsequent sessions, so you have to import the profile you created each time.