It's version 3.5.1.1679, according to the About MonoGame Pipeline Tool dialog.
I created a new Windows project called Game1, double-clicked Content.mgcb in VS which opens up the pipline tool. I added one file to it, I don't think the file type matters as I've tried with a .wav and a .png and they had the same problem. I've attached the png, it was called debris.png and I tried saving it in the root Content folder, or creating a subfolder for it, with the same results:
I've tried switching between HiDef and Reach profiles, no difference. Click Build or Rebuild, it asks me to save the project, I click Yes then nothing happens. Try again, nothing happens. Clean works though.