Hi Breno,
Because you have the same trouble on 2 computers, and because nobody else has reported this problem despite many downloads, and because I have run the program successfully on multiple computers with a genuine Arduino Due and have also tried a cheap Chinese Due, but have not tried it with the same Due version as yours, I think you could be right suspecting your Due. It would be good if you had another one to try, wouldn't it?
If anyone else has had this problem, we would like to hear from you!!
Cheers,
Bruce.
PS: Did you install Processing 3? It looks really similar to the Arduino GUI, doesn't it?

Hi Breno,
I suppose I should have guessed the answer was yes. I suggest checking if you can control the DUE using Arduino's serial monitor at 115200 baud. If you can, then I would not expect the com rate to be the problem. If you can't, it would be easier to just change the rate in the .ino file at first, to see if it helps (using the monitor).

Hi Breno,
You appear to have forgotten to answer the following question:

Will the GUI operate WITHOUT the DUE connected? (just to open or draw waves, or access the help file, etc.) If the answer is no, then your suggestion and question may be irrelevant, but I'll answer it anyway:

The GUI program was created using "Processing" - the program that Arduino was originally based on. So in order to change the com rate you would need to install Processing 3 on your PC so you can change the DueArbitraryWaveformGenerator.pde file (found in the source folder). If successful, you could then "export the application" to create the DueArbitraryWaveformGenerator.exe file. (as well as changing the Arduino .ino file)