I had an R4 card with NDS games on my 3DS XL before installing the CFW on it; after installing the CFW and rxTools everything worked nice on the EmuNAND, except for the R4 card, if I try to open it from the EmuNAND, it crashes and my Nintendo shows a message telling me to restart it. I imagined this could happen before trying to open it, so I tried to access tot he R4 card through the SysNAND, it opened its menu and everything looked fine, except that when I tried to access a game, it went to the R4 loading screen for a moment (as it always do) and then it went to white screen on both screens. I had to restart my console having pushed the power button, then I tried again and I found that my R4 opens Homebrew apps like emulators or Super Smash Bros. Crash, just not the games. After that I noticed something else, every time I access to the R4 card it disables my rxTools for launching from the Profile menu; I have to launch it from Internet again and then I have to reinstall the MSET ROP from FBI for it to work properly again.
Obviously my rxTools is on an SD card that I put on my 3DS' SD slot and my R4 has it's own microSD.
Thanks.