I had the same problem, removing menuhax did the trick.
Huh, that's weird. I loaded a9lh on my o3DS using menuhax.
I have had problems with certain homebrew launchers not working with homebrew that works on kernel exploits. Mashers' grid launcher had issues with FBI & sysUpdater, but using the original worked fine, with and without workarounds (e.g. loading FTP-3DS)
If you have trouble with a9lh on alternate homebrew launchers, try using the original from the homebrew starter pack. ctrBootManager will work fine too - in fact, I set up a9lh using ctrBootManager then smea's homebrew launcher.