Make sure that you're using the proper files associated with the ROP exploit you're using.
Try to do this:
1. Put Gateway's most recent Launcher.dat file on your SD Root.
2. On the 3DS, use the web browser to go to "go.gateway-3ds.com" and then use that exploit to make a NAND backup (if you haven't already). Copy NAND.bin over to your computer in case anything goes wrong.
Format EmuNAND in the menu too. This will wipe your SD card and reserve ~1GB for the operating system (~2GB if N3DS) so make sure you back up your files first.
3. Download the latest RXTools nightly from this link:
https://lavanoid.github.io/ (Click Download, then scroll down to the very bottom-most dropbox upload. Ensure it's the most recent by checking the date modified)
4. Install
Python 2.7 on your computer, then go to RXTools' .zip, extract the "release" folder to somewhere on your computer. Enter the release folder, then copy the "rxtools" folder to your SD card's root. (SD:/) Then in the Tools folder, double-click cdn_firm.py. It should generate a "firm" folder, which you should put in "SD:/rxtools/".
5. Google and find "slot0x25keyx.bin" and put that in SD:/ (SD card root)
6. Go back to the .zip, at "release\Tools\fbi_injection\jpn\v0" and copy "fbi_inject.app" and "fbi_inject.tmd" to your SD card's root.
7. Download FBI, and put the FBI.cia file in your SD root, too.
8. Put the SD card in your 3DS, then run System Settings. Go to Data Management and it should format your SD card.
9. turn on your 3DS web browser, and clear your cache/history. Turn off your wifi and go to "
https://dukesrg.github.io/?mset/rxinstaller.bin". The website will fail, and this is okay. Close out of the web browser and reboot.
10. Turn on your 3DS, turn on Wi-Fi, and immediately run the web browser. Your web browser should crash, and that should install the ROP exploit in MSET (System Settings).
11. Hold L (or was it R? it's probably R) while RXTools is booting up and you should get in a menu. Attempt to inject FBI to your SysNAND.
12. Run RXTools Pasta Mode (aka DevMode) and run Health And Safety. If it worked, you should be in FBI. Use FBI to install the newer version, FBI.cia.
(Am currently editing this, but go ahead and do this while I type up the rest of the instructions)