Are you using EmuNAND? If not, unselect the "Use second emuNAND as default".
Also, something similar happened to me with my updated SysNAND. Since I had no backup of my SD card (only of my NAND), restoring the NAND didn't do a thing. So, what I did was formatting my System from System Settings, format the SD card and only add the A9LH needed files, and re-installed everything back again. That solved the problem for me.
I had something like that happen with my o3ds xl on Emunand with Menuhax (prior to switching to A9LH)...only some of the apps were showing and I restored an EmuNand Back up from May and so far I don't have a problem with homemenu display anymore...Do you have a recent nand back-up?