Have you tried using an Alkaline battery instead of a Carbon Zinc battery? Carbon Zinc batteries should only be used in very low current applications. Carbon Zinc batteries do not deliver much current and have a much lower capacity than alkaline.
See this article on 9v battery comparisons http://www.powerstream.com/9V-Alkaline-tests.htm He tested a Panasonic Super Heavy Duty battery (wich most likely has a better performing Carbon/Chemestry than the standard Carbon Zinc Panasonics) an when pulling 100mAh it had a mesured capacity of only 52 mAh
Have you that maybe the board is not getting enough current? I’d suggest you to see the current given by the battery, according to the Hardware guide:
“The battery should be at least 300 mAH capacity, due to the 100 mA charging current.”
Also, take a look at this thread Edison Mini Breakout Board Battery you may find useful information since the original poster is also using a 9V battery in J21.
Additionally, J21 on the mini breakout board accepts a supply voltage of 7 to 15 VDC. So the voltage sag caused by hooking up the Edison, also puts a Carbon Zinc 9v out of the operating spec of the mini breakout.
Alkaline is working fine. I learned something new about batteries that carbon zinc is actually the lowest grade, hence being really cheap.
However, I am looking at getting some 3.7V, 3000mAh 18650 lithium-ion batteries in series to power my mini-breakout board.
9V Alkaline just doesn't have enough capacity for my application.