Session ending before timeout is an issue faced by many developers who use IIS 6. I have found that in most cases, this is caused when you set the recycling of worker processes using IIS manager.
Check this cool post to understand this better.
Here are 3 quick suggestions to troubleshoot this issue (assuming that you are using In-process mode - ASP.NET session state):
1. Check and see if you have configured recycling of worker processes
2. If you are maintaining cookie enabled sessions, check if the cookie is not getting deleted/modified at the client end.
3. Check to see if IIS/Application Pool is not getting restarted at regular intervals. Your application pool will restart if your global.asax or the web.config/ machine.config changes
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