In Formativ versions prior to 2.0.1, the Formativ installer would disable the association between VBS/VBE files and the Windows Script Host. However, we changed that operation in 2.0.1 and it should not do that any more.
As you know already, you can re-assign the association from the Formativ Windows Control Panel applet – press the ‘restore association’ button under the additional security section (and ensure the ‘disable association…’ option is unchecked).
If this is not solving your problem, it would appear that the Registry entry controlling this setting is being rewritten by Citrix for some reason. Perhaps a master(?) Registry entry is not set correctly and is propagating when a Citrix user logs in?