Hi GigasightMedia,
Sorry for the delay on this issue. I found out today that some of our engineers actually found and fixed this issue a few days ago. There was apparently a circular dependency that could occur between a couple modules when building the Engine, that resulted in this issue. From information that the engineer I was speaking with provided I was able to reproduce the issue by deleting the Engine/Binaries/DotNET/AutomationScripts folder, then building the AutomationTool project. Doing that gave me the exact same error messages that you reported seeing, and building the AutomationTool project a second time completed successfully.
Unfortunately the engineer was unable to provide me with the exact change that they implemented, so I am not sure exactly what fixed this issue. I did try to reproduce the issue in our latest internal version of the Engine using the same repro that I mentioned above and the AutomationTool project built successfully on the first try, so it looks like the issue should be corrected in a future release version of the Engine.
I am still not sure what would cause the issue to occur for you and some others, but not for me unless I took some very specific steps that I do not believe you are taking. That is still something of a mystery.