I have this same issue and message today on Windows 7, and my system tray shows Agent 1.1.87-version fca3237.
Sketches compile and run fine with the online and offline IDE). However, I do receive a "SAM-BA operation failed" error message each time. Maybe this is related somehow.
"We were unable to upload the Crypto Chip configuration code to your board.
Are you sure the Arduino board is connected properly with a USB cable? Try disconnecting and reconnecting it. If that doesn’t work, try pressing the Reset button twice. You may also write us on the Forum."