The "bossac.exe -h" problem with Due on ALL uploading

This problem of the "bossac.exe -h" message is well enough known but nothing I have read on the Internet describes the full scope with which I am seeing it. Basically we wish to add RFID readout to a project under development but to get up and running we just want to read RFID tokens. To do this we tried various software offered on the Internet and on a Due we get the bossac message. Well, there does seem to be a problem because some sites claim no suitable software for a Software Serial method has been provided. Conversely I realized there are other possibilities with Due because it has its own extra serial ports, 3 in all and thought, a perfect solution. Better than UNO. Ha, Ha! Trying a sample program promptly brought that ugly bossac complaint with a notification about extra arguments which are invisible to us. Now I accidently tried to run the skeleton sketch given to us by the IDE (1.6.7) and this empty program still gives that message. Suddenly it is clear the problem goes far beyond serial commands. As I worried how it could be so bad I realized the Due we were using worked on our developing program until now, as if maybe there was a "repair" downloaded as an automatic update which inserted this error message into a previously working environment. Is such a problem known? How can one fix an argument when there are no commands beyond the minimum "void"? And how can programs be once more made to run on the Due which offers some real advantages over UNO, for example? And finally, I have read others report this kind of trouble and got rid of it with earlier and later versions of the IDE. I called up the new download for IDE1.6.9 and it wants to destroy all program data in the directories where such data are normally stored. Even Microsoft can do better than this! Why would anybody write software this way?