Thanks for the quick feedback. I have noticed that most of the problems are with the command line user interface; I've replaced it with a little WinForms thingy:

https://code.google.com/p/csharp-dessist/

The latest package is here, could you try again and let me know if the simple UI helps avoid some of your errors?

https://code.google.com/p/csharp-dessist/downloads/detail?name=csharp-dessist_2.0.zip