Thanks for your post. You don't need to register any of the RedGate assemblies or place them in the system32 folder; in fact I'd recommend avoiding this as it could introduce problems when we upgrade the assemblies.
More than likely there is a missing dependent assembly. When you distribute a SQL Toolkit application, you have to distribute the assemblies specified
in the Toolkit documentation.
The other possibility is that you use the Data Compare engine. If you are using the Data Compare API, you need to ensure that all of the assemblies come from the SQL Data Compare distribution because the dll versions vary between the SQL Compare and SQL Data Compare distribution so that the Data Compare dlls all need to be kept in the same directory as your console application.