I'm not sure what's causing this, but I'd tried chown and chmod with all privileges, but this. splashtool is in the devkitpro directory (/opt/devkitpro/splashtool). I've not had this issue before with this stuff:
godreborn@GODREBORN-LAPTOP:~/fastboot3DS$ make
make[2]: '/home/godreborn/fastboot3DS/arm9/fastboot3DS9.bin' is up to date.
make[2]: '/home/godreborn/fastboot3DS/superhax/superhax.bin' is up to date.
banner.png
menu.png
make[2]: splashtool: Permission denied
make[2]: *** [/home/godreborn/fastboot3DS/arm11/Makefile:168: menu.spla.o] Error 127
make[2]: *** Waiting for unfinished jobs....
make[2]: splashtool: Permission denied
make[2]: *** [/home/godreborn/fastboot3DS/arm11/Makefile:168: banner.spla.o] Error 127
make[1]: *** [Makefile:115: all] Error 2
make: *** [Makefile:44: checkarm11] Error 2
godreborn@GODREBORN-LAPTOP:~/fastboot3DS$ make
make[2]: '/home/godreborn/fastboot3DS/arm9/fastboot3DS9.bin' is up to date.
make[2]: '/home/godreborn/fastboot3DS/superhax/superhax.bin' is up to date.
banner.png
menu.png
make[2]: splashtool: Permission denied
make[2]: *** [/home/godreborn/fastboot3DS/arm11/Makefile:168: menu.spla.o] Error 127
make[2]: *** Waiting for unfinished jobs....
make[2]: splashtool: Permission denied
make[2]: *** [/home/godreborn/fastboot3DS/arm11/Makefile:168: banner.spla.o] Error 127
make[1]: *** [Makefile:115: all] Error 2
make: *** [Makefile:44: checkarm11] Error 2