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    For those times when it doesn't work, is it possible that the requests were existing ones being served by the old app pool via overlapping rotation? Not sure of the uptime requirements of your site, but you could try disabling overlapping rotation and including an app pool recycle command in your deployment script. Commented Apr 4, 2013 at 13:47
  • No, all subsequent requests is served from the old webroot, even an application recycle will reload the application from the old root. An IIS reset is the only way we have managed to restore it. It's like the applicationHost.config is updated (since IIS manager shows the correct path), but the IIS server itself works from the previous configuration... Commented Apr 4, 2013 at 13:49
  • I can not find a mention of it in applicationHost.config, so I assume it's the default "false"? Commented Apr 4, 2013 at 13:59
  • OK, was thinking if disallowOverlappingRotation = true, then old app pool might not be shutting down due to a long-running thread or something. Which is why IIS Reset would be required to fully clear it. Interesting question -- will be curious to see what answers show up. Commented Apr 4, 2013 at 14:01
  • Bear in mind an app pool recycle isn't the same as stop/start. Have you tried this method? Bear in mind, this will kill all current connections and make the site unavailable (error 500) until the app pool is restarted. Commented Apr 11, 2013 at 14:35