OK I've solved it.... and there are obviously different RCM loaders that work differently so this might not work for you.
**UPDATE: I reformatted the RCMloader in fat format and loaded all the files back onto it and now it works and actually changes between loads like it's suppose to
This advice works.
I formatted FAT (restored default allocation table size). Restored the files you added and it worked.
However as soon as I tried to remove the folders I didn't need my RCM loader wouldn't see them. Also if I added or renamed a folder RCM loader won't see it.
So at the moment I have the Atmosphere/Hekate folder with Fusee.bin (Renamed to payload.bin).
And I put the Hekate.bin file in the REINX folder. On this model of RCM loader it won't let you rename these folders if you try only the first folder (alphabetically) will work.
On my old RCM loader it wasn't a problem.... you could call the folders whatever you wanted too, and the "+" just cycled the folders alphabetically.
For me these are really the only 2 payloads I really need. I occasionally use Tegra explorer and the only other payload is lockpick (but I doubt I'll ever need it again, I'd be on a PC if I did).
However if someone is reading this and may require other payloads in the future (say android or windows etc.) .... you can copy the redundant folders into one of the payload folders your going to use just to keep the file structure safe and recoverable. The device won't see the other folders and simply launch the payload.bin
One more thing.... you need to use the folders in order. So you have to Put your primary payload in the Atmosphere_Hekate folder then your secondary payload in in the REINX folder etc. If you deleted say the REINX folder and tried to use the SXOS or USER folders it won't change to the next folder as it's not found the folder its looking for (alphabetically) . So it just goes to the default folder (launch.txt).
You can change the default folder in launch.txt.... which can point to any folder. However if you don't use the fist ones (alphabetically) that becomes the only Folder your RCM loader will be able to see.
I hope that helps someone.