There are a few Enterprise Portal dlls that can be unusual with regards to applying hotfixes - when deploying kernel hotfixes they'll be automatically updated, but there are some application fixes which include a new webParts.cab, and then some of the dlls may need to be manually deployed/installed. The dlls in question are:

  • Microsoft.Dynamics.Framework.portal.dll
  • Microsoft.Dynamics.Compliance.InternalControlsManager.dll
  • Microsoft.Dynamics.WebParts.dll
  • Microsoft.Dynamics.Framework.Portal.CommonControls.dll

Our colleagues in the US have written a great post which explain the full details on exactly what to check in which places so that you can get everything correctly up to date:

http://blogs.msdn.com/b/axsupport/archive/2011/07/29/enterprise-portal-ep-dlls.aspx