Why are you using Arduino IDE 1.6.9?
Why are you using Arduino AVR Boards 1.6.12?
There have been some problems with backwards compatibility of Arduino AVR Boards and other hardware packages in the past. You can be reasonably certain that the version of the package bundled with the IDE will be fine but updating can be problematic. I have done some work to try to ensure backwards compatibility but since you're not using the latest AVR Boards version you might not be benefiting from those changes. I'm could most likely figure out the specific problem you're encountering but I'll wait for your reply to my questions above to see whether that information would even be relevant.