If you have users reporting session timed out even though they were using the application, then it must be due to JRE version which client is running. It is better to run the same version of the JRE that is installed on the server or the latest one.
If the above step doesn't help do the following for the JRE;
1. Go to: Start > Control Panel > Java > Advanced > Java Plug-in
2. De-select the option "Enable the next-generation Java Plug-in"
3. Restart the browser and check the application, the timeout should not happen again.
To increase timeout from the server, do the following;
1. Change profile option ICX: Session Timeout to 90 min from the default value of30min.
2. change s_oc4j_sesstimeout value to 90 again in context file.
3. Stop the appliation services and run adconfig.
4. Start application services and check the application.