Are you on 2.1? The installer should work fine if you have both arm11 and arm9 binaries in 2.1 - just make sure you do not have other otp.bin files in your A9LH folder. It should not error like that unless you are not in 2.1 or you might have wrong otp file on SD.
Also if you ARE on 2.1 indeed; before this is sorted out do not keep your system on and in sleep mode; always shut it down there is possibility that N3DS system can brick for entering deep sleep or something in 2.1