I am also having this issue with MSVS2013 Update 4 and EF 6.0
The message I was getting was:
there was an error running the selected code generator.
A configuration for type XXXX has already been added ...[]
I have a model with around 10 classes. I scaffolded elements at the beginning of the project with no problems.
After some days adding functionality, I tried to scaffold another class from the model, but an error was keeping me from doing it.
I have tried to update MSVS from update 2 to update 4, comment out my OnModelCreating method and other ideas proposed with no luck.
As a temporary way to continue with the project, I created a different asp.net project, pasted there my model classes (I am using fluent api, so there is little annotation on them) and successfully created my controller and views.
After that, I pasted back the created classes to the original project and corrected some mistakes (mainly dbset names).
It seems to be working, although I suppose that I will still find mistakes related to relationships between classes (due to the lack of fluent configuration when created).
I hope this helps to other users.