My software setup is quite different (new 3ds, AuReiNand, 10.6 sysnand, 9.2 emunand, unedited payload, Gridlauncher, no CTR). Any number of things could be causing your problem, but I don't think it's the hax.Hmm interesting.
I run on a new 3DS with 9.2E sysNAND and 10.6 ReiNand emuNAND. I definitely have updated the payload too as it says *hax 2.6 Gamma in the debug screen however I did manually edit my payload to point to bhbl.3dsx instead of boot.3dsx to comply with my CTR setup. And I haven't updated Homebrew Launcher Loader in ages so it might be related to that probably.

