That is sure a strange issue. You're building MassExplosion's fork, right ? (https://github.com/fox8091/CakesForA9LH)
Try building using this: make build/main.bin
And use build/main.bin as an arm9loaderhax.bin payload.
Try building using this: make build/main.bin
And use build/main.bin as an arm9loaderhax.bin payload.
I wonder if doing it on OS X is causing the problem