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I watched a guy (doesn't work with me, works for another company) today duplicate a SQL Reporting Services ReportServer virtual directory by saving the existing one to file using normal IIS and creating a new one. There is a decent enough reason for doing this, but that doesn't matter.
This failed, badly. Reporting services kept complaining about not being able to find the <server path>/REPORTSERVER/bin folder.

The solution to this actually was to remove the folder he created, use reporting services configuration tool to create a  new one and then do an IIS reset (thanks Bruce for the iis reset). This created a perfectly working report server folder and with the original one left untouched it continued to work correctly.