System.Net.WebException: The operation has timed-out.

I have a very simple web service built with Java and deploy on Websphere server. The WS just receive a string array and return an integer value.

I have another .Net client which has to call this WS, the client is deployed on a windows 2003 based Citrix MPS server, and all users has to logon to this server in order to use the client. The MPS server and websphere server is on the same network, there is no network problem between them.

What I have spent two months to solve is that some users can call the WS through the .Net client perfectly, but some of users always fail to do that with this exception:

System.Net.WebException: The operation has timed-out.
  at System.Net.HttpWebRequest.GetRequestStream()
  at System.Web.Services.Protocols.SoapHttpClientProtocol.Invoke(String methodName, Object[] parameters)
  at EDocSharp.com.group.asia.cnws01.FileIndexValidatorService.checkNewFileIndex(String documentTypeId, String[] indexValues)
  at WSValidation.checkNewFileIndex(String documentTypeId, String[] indexValues)

or

System.Net.WebException: The operation has timed-out.
  at System.Web.Services.Protocols.WebClientProtocol.GetWebResponse(WebRequest request)
  at System.Web.Services.Protocols.HttpWebClientProtocol.GetWebResponse(WebRequest request)
  at System.Web.Services.Protocols.SoapHttpClientProtocol.Invoke(String methodName, Object[] parameters)
  at EDocSharp.com.group.asia.cnws01.FileIndexValidatorService.checkFullIndex(String fileId, String targetStatus, String[] indexValues)
  at WSValidation.checkFullIndex(String fileId, String targetStatus, String[] indexValues)

I think the problem is somehow come from specific user session, so I tried to build a standalone webpage using Javascript to call the WS to further study the problem. However, the user encounters problem in .Net client can still call to the WS using this webpage.

So I think the problem is come from the System.Web.Services library, even I cannot read its source code and do not know it is fail in some user sessions.

Anyone has idea about the problem, or how can I investigate what's going on in the System.Web.Services library in something like debug mode to fully understand how user session / profile affect this library