I am owner of a RCMLoader One first version, and can load either Hekate 5.5.6, Atomosphère 1.0.0 (latest) injecting Hekate and FUSE.BIN payloads respectively, you must be careful to rename payload.bin and put on a folder on the RCMLoader, and pressing the button change the corresponding color-folder. I also use the RCMLoader to inject TegraExplorer 4.0.0 and LOCKPICK_RCM_1_9_4 with no problem at all.
you should try to update all your homebrew by hand an download the latests releases from his repository. As I note your problem was a outdated injector/SD Files combination.
the same goes to the
sigpatches if you use it, update it manually.
I am not against the prepacked setups but sometimes they aren't updated to latest files and the result is only works with exactly the combination of CWF and Homebrew they was created, and if you update only a component can get inconsistencies for others pieces of software.