The solution to this problem (found by my colleague Philip Aylward) was sufficiently obscure that we thought we would share it ....
We were having difficulties executing our in-house developed software running from a cmd prompt in Windows 7 (32 & 64bit). The application would hang and was irrecoverable. We used process explorer to view the processes which were associated with the application. There was an instance of conhost.exe and the application.exe. The only way to kill the application, once hanging, was to kill the conhost.exe process.
A description of the way conhost.exe works is given in http://blogs.technet.com/b/askperf/archive/2009/10/05/windows-7-windows-server-2008-r2-console-host.aspx. We looked at the relevant processes and also used the Analyze Wait Chain feature of Resource Monitor to determine which process was waiting. This showed that the application.exe was waiting for the application.exe so this did not help.
A search on technical websites revealed a comment regarding keyboard layouts and the use of additional languages (http://serverfault.com/questions/26217/win7-command-processor-cmd-exe-really-slow/210961#210961). We removed any additional keyboard layouts leaving just one (English - United Kingdom).
On reboot, the application ran normally.
