Under certain circumstances Java properties might not save to the User Store on Logoff. 

Java saves the required information in the folder: Appdata\locallow\sun\java\deployment
The below steps will help with configuring the Citrix Profile Managment policy as follows to to synchronise the Java folders:

Citrix-Profile Management > File System > Synchronization

It is recommended to configure the "Directories to synchronize" AND/OR "Files to Syncronize" policy setting (link), this setting should be located under File System > Synchronization

Directories to Synchronize should be updated to include the folder:

• Appdata\LocalLow\sun\java\deployment
• AppData\LocalLow\Sun\Java\Deployment\ext
• AppData\LocalLow\Sun\Java\Deployment\security

The setting Files to Synchronize, must include the following files:

• AppData\LocalLow\Sun\Java\Deployment\deployment.properties
• AppData\LocalLow\Sun\Java\Deployment\security\exception.sites
• AppData\LocalLow\Sun\Java\Deployment\security\trusted.certs

• http://www.carlstalhood.com/citrix-profile-management/#mandatory
• http://discussions.citrix.com/topic/295280-sun-java-folder-in-appdata/