But do you have Luma's arm9loaderhax.bin in the SD card? If you don't, I'm pretty sure that's your problem. I don't know anything about this boot.bin thing though, so I guess I'll go read about it. In the meantime, try putting the a9lh.bin in your SD card and see if it starts working.
Edit: OK, sounds like you're right, someone asked specifically about payloads in the Shadownand thread. Maybe you have a faulty SD card? Is there a way you can tell you're in Luma after you boot up, and not in the CFW installed to the NAND? Maybe the SD is really slow or something, and doesn't get read in time to boot Luma, so boots the mini CFW, and then later your games show up.