I had the same problem the first time I tried to download Beta 3. It was while the server was overwhelmed (before Brad switched the files to a faster server). I noticed that a large number of files never got brought down and caused a number of problems on my machine, including the "missing xxxxxx.dll" message on one attempt to start the game. After Brad put the game on the faster server I did a fresh download into a clean and empty directory and that cured the problem.
BTW, I think this shows up an issue with the DGM. If the server is overloaded and the DGM gets a long period of no data it looks like the DGM gets all mixed up on what files it has.
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