Going into RCM, and using your bootloader to inject a payload, are two different things.
RCM, short for Recovery Mode, is the black screen you get when you use the jig and various button combinations (auto-RCM also goes straight to RCM when you boot up).
I know TegraRCMGUI says you were successful in injecting a payload, but I don't know if TegraRCMGUI were to throw an error if Switch is not on RCM. (in essense, I don't know when and how it throws errors)
With my explanation out of the way: once again, are you able to get to RCM?
Fully delete the folders and the bin you have (maybe keep safe backups elsewhere on your computer).
Then, redownload the Atmosphere folders into your SD, and redownload the bin for your bootlooder.
[I'm asking you to delete the folders, cause sometimes people just combine folders, and that could be bad. Some contents are not meant to be mixed and matched]
Speaking of bootloaders, try using the latest TegraRCMSmash instead (to see if that makes a difference).
It's real simple to use:
1. Have your Switch on RCM
2. hook up the USB-C cable between your Switch and your PC
3. Drag the fusee-primary.bin onto the file icon, and it'll inject the payload for you.