Are you using 1.6?
If that's the case, the homebrew softreset is causing the problem.
What happens is AKAIO changed the ARM-7 code of each piece of homebrew as it's loaded (note that it does not actually modify the .nds file) and this is fine for 99% of all pieces of software.
However, moonlight built some security into Moonshell 2 so that if the Arm-7 code is modified, Moonshell will refuse to boot.
It's not that they are angry at each other, both groups just created some conflicting features. It's expected that this issue will be fixed soon, as moonlight has no problems with the soft-reset code (IIRC).