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Источник: http://sumitax.wordpress.com/2010/10...-steps-ax2009/
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Here are steps for WorkFlow installation  on Windodows Server 2008 R2:

1. Run the AX2009 set up and select the EnterPrise Portal  Website to be used for WorkFlow.
2. Delete the application from the IIS . This is should be something like  MicrosoftDynamicsAXWorkFlow50
3. 
   Added a “Virtual Directory” to the same site and named the new virtual directory with the same name of the deleted application.
4. In the Physical path of the virtual directory, point to the installed worklfow folder .This should be under AX Folder .
5. Convert the new “Virtual Directory” to “Application” by right-clicking that directory and clicking “Convert to Application.
6. Go to EnterPrisePortal application  ans select “Authentication” under IIS section.
7. Enable the ASP.NET authentication and Windows Authentication.

Источник: http://sumitax.wordpress.com/2010/10...-steps-ax2009/