I am running Arduino IDE on OS X.
I am having problem with yocto 2.1:
When the Edison board is running yocto 2.1, i am unable to upload sketch through Arduino IDE.
but when the Edison board is running on yocto 2.0, i am able to upload the sketch through Arduino IDE
Which Arduino IDE were you using? I just tested the Arduino IDE 1.6.5 with the x86 boards installed from the board manager on OS X 10.11.2 El Capitan and I was able to successfully upload the blink sketch to my board. I'm currently using the latest image found in https://software.intel.com/en-us/iot/hardware/edison/downloads Intel® Edison Downloads.
Have you tried with Arduino IDE 1.6.5?
Were you able to flash your edison board with yocto 2.1 on your mac? and were you able to see your board in the flash tool window?
I am attaching a screenshot of whats happening to my flash tool as well, I was able to flash it using terminal but not with the flash tool.