最近SharePoint 2007迁移到2013的时候，碰到创建应用程序时IIS端口文件夹下没文件的问题，网上找了大把的原因，终于在这里找到了解决方案：
Fix:
1. Open IIS on the SP2013 host machine.
2. Navigate to the Application Pools
3. Right Click "Sharepoint Central Administration v4" and click "Advanced Settings"
4. Scroll down to "Shutdown Time Limit" and change it from the default time limit to 300 or 400 seconds.
5. Press OK, and then perform iisreset.
This should resolve your problem.
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Workaround:
1. After the site fails to create and SP timesout for the shutdown time limit being exceeded, Refresh the Web Applications list and find your newly created (non-working) WebApp in the list.
2. Select your Web Application and Click on Authentication Providers
3. After the Authentication Providers dialog opens, Click Save.
Performing this action will cause SP to recreate any necessary files in the Virtual Folder for that WebApp
主要的原因是因为服务器的性能不够，导致操作超时，所以方法就两个，1个是加超时时间，2就是通过重新保存用户权限来自动重新创建。