Flash Tool Lite 5.3.2 doesn't find the board on Mac OS X El Captain (10.11.1). I tried on Arduino and mini with the same result. On a Mac with previous OS (10.10.5) it works without any problems.
I'd like to know if Intel is aware of this problem.
Yah intel is aware of Flash tools not working under El Capitan.
Since its so hard to find right pages regarding edison, im not gonna search but i know there's a page where you can download Flash Tools where they also note it not working with OSX 10.11
EDIT: just had to search anyway So.... after 13min, i still can find that page where they stated misfunction of FTL on osx
As danelk mentioned Flash Tool Lite may not be compatible with OSX 10.11.1. According to the https://software.intel.com/en-us/articles/flash-tool-lite-user-manual Flash Tool Lite User Manual, it is officially compatible with version 10.9.5. So, other version are not validated.