When you are using a VSTO enabled Word Template inside a SharePoint custom content type you have to be careful which actual .DOTX file you use within the SharePoint custom content type.
- DO NOT – use the .DOTX from your VSTO Visual Studio project directory
- DO USE – the .DOTX from the the project's ClickOnce publish location.
The key point here is that until you have published the VSTO project via ClickOnce the .DOTX template does not know where to find the deployment of the associated assemblies. The copy in the project directory never actually knows this location as it is just a source file not a deliverable.