The "hotfix" build contains the same assemblies as the other distributions. The "hotfix" distribution is a distribution meant to fix an issue with a previous version. It contains just the assemblies that you can drop in your project, update your references, and get going. It may not sound very appropriate for a v1.0 release if you don't consider the beta releases we had before that.
Jaime, can you post more details about your manifest exception, possibly a screenshot? The only way I can imagine that exception appearing is if you have a reference to an older version of Telerik.Windows.Controls, Telerik.Windows.Data, or Telerik.Windows.Controls.Input in your project. I'd like to reproduce the issue on my end and investigate it in detail, and step-by-step repro instructions will be much appreciated. Thanks!
the Telerik team