Query time out expired problem

Hi guys.

I have a Windows application that execute some queries on a database (obviously). They are very hard queries, so, to be sure my application don't generate "Timeout expired" error, I set CommandTimeOut property of SqlCommand object to 3600 seconds. Although I set a so big timeout, sometimes, my queries generate "Timeout expired" error after 4 or 5 seconds of execution. Why?

Thanks