I also tried flashing and had the same result as you, both with or without startup code. Maybe there is a conflict with code in the LIB. I realize that it will be just a waste of time to try to make something work together with a closed-source component. So I will either go back to the free 1.1 version or wait for you (or BenF) to release some more code 
Meanwhile I will look at making a dfuse firmware loader for Linux so that we will not need a Windows machine or license to flash the DSO. Hopefully it will be enough to modify the dfu-util a bit. Probably someone has done this already, but I haven’t found any published code.