Which project complains about the references, is it one of the LLBLGen generated projects, or the application consuming the generated code?
Please make sure of the following:
1- The consuming project is referencing LLBLGen 5.x dlls
2- The consuming project is referencing the recently generated code
3- The recently generated code/projects are referencing the same LLBLGen 5.x dlls
4- All projects are on the same .NET framework version.