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Ok so new answer. First of all, you are still using OpenCV2.4.3 since that is the dll type the exe requires when I am starting up your training system. I have switched to OpenCV2.4.6 (do this also) and compiled against the newest libraries, used the training algorithm on your data and it works perfect.

Be sure that your result folder is manually created before running the algorithm, else it cannot write data to it.

Here you can find the command I used to start the training, and the actual result of the first 2 and a half stages.

Don't mind the fact that you will not get the calculation time for the previous stage, it is something that I adapted in the source code, in order to see how my progress was going.