I know that this is probably a given, but I have to ask just to cover all bases. Do you have Launcher.dat on the SD card? Even if you're using GW.3dsx, you have to have the Launcher.dat file to boot into GW Mode. All GW.3dsx does is load Launcher.dat.
This is the exact setup that I have on my 3DS that works perfectly for me.
- SysNAND 9.2/EmuNAND 10.7
- GW.3dsx in SD:\3ds\GW
- No files other than firmware.bin (for NTR use) in SD:\luma\
- arm9loaderhax.bin (Luma3DS), Launcher.dat (GW), and boot.3dsx (CtrBootManager) in SD:\
- boot.cfg set up to launch GW.3dsx
- The following options turned on in Luma3DS configuration: Autoboot SysNAND, Force A9LH detection, Show current NAND in System Settings, Show GBA boot screen in patched AGB_FIRM. Everything else is turned off.