As part of the FinalBuilder install we check which version of TFS is installed, and set bindingRedirects in FinalBuilder.exe.config to reference the latest installed version.
If you have upgraded Team Explorer after installing FinalBuilder, FinalBuilder will still be referencing the old assemblies. For example, you may see a TFS error such as:
F253023: You must update your client with the Forward Compatibility Update in order to connect to the Team Foundation Server that you selected
Re-running the FinalBuilder installer will fix the binding redirects.