OK found it. If anybody have the same problem,
I've wrote a very simple programm, to get all the overgiven parameters, so: now it works... Oh my god, it's to early in the morning. So if you want to know what bossac gets:
1) Write a simple C-programm callec "bossac": The Code is also very simple:
int main(int argc, char **argv)
printf("%s\n ", *argv++);
2) go to -> arduino->hardware->tools
3) rename the programm "bossac" to "~bossac"
4) copy the executable from your programm(also must be called bossac) to this folder your rename the other programm
5) start the arduino-IDE from the shell and write any code to the DUE( real flashing must not work!!)
6)in the shell you see the parameters given to bossac from the Arduino IDE...