If your users are getting timeout errors for interacting with a web app through an iFrame portlet on Sun Java System Portal Server, then you got two theoretical workarounds:
1. Increase session timeout to a larger number. This will increase resource footprint (mainly memory) on Portal Server and may cause inefficiencies. So, if you have plenty of RAM and you are not running into performance issues related to memory, you can consider this option.
2. Build a heart-beat or ping-back mechanism. This can be done in two ways.
2.1 One is to build a proxy servlet that run within the Portal Server instance. Instead of having user’s browser interact with the web app that live within the iFrame, have the browser talk to the proxy servlet that forward each request to the actual web app. The amount of extra network traffic will depends on how chatty your web app is. This will also require you to modify your application’s logic.
Let me know if you have a better idea.