<p>We have very strange problem, one of our applications is continually querying server by using .net remoting, and every 100 seconds the application stops querying for a short duration and then resumes the operation. The problem is on a client and not on the server because applications actually queries several servers in the same time and stops receiving data from all of them in the same time.</p>

100 Seconds is a give away number as it's the default timeout for a webrequest in .Net.
I've seen in the past that the PSI (Project Server Interface within Microsoft Project) didn't override the timeout and so the default of 100 seconds was applied and would terminate anything talking to it for longer than that time.
Do you have access to all of the code and are you sure you have set timeouts where applicable so that any defaults are not being applied unbeknownst to you?