Hi Samir;
FWIW: Many of my Canadian Government clients run their PB application EXE's from a W2008R1 server as it is the standard O/S at the moment on their servers. Some departments have between 2,000 and 4,000 concurrent users of a PB application EXE being launched and not one issue like you have experienced.
Sounds to me that your issue might have its roots in an improperly configured server, network issues and maybe even the way you packaged your application EXE. I would begin with relocating the application EXE to another first and see if that remedies the situation.
BTW: What build of PB are you using?
Regards ... Chris