First of, I don't know if citrix adds to this issue.
However, WinForms applications store their settings specific to the version of the application. If you increase the version number of your application you also must migrate/update your settings:
Especially have a look at the remarks section. This applies to local and roaming settings.
Maybe this article can help you:
http://www.ngpixel.com/2011/05/05/c-keep-user-settings-between-versions/