Thank you hank315 for trying out my encoder
Ok, regarding the failure of the encoder to use skip mode in unicolour macroblocks: lambda was 0 for quant = 1 so the bit count of the macroblock was not taken into account when determining modes. -Fixed in SVN. Black bars should be skip now.
I also added the ability to specify text files containing 64 values as Intra or Inter Quantization Matrices to the application so there is no need to make changes in the source code anymore when trying QMats out.