No. the only Retroarch related folders are SD:/Retroarch and SD:/wiiu/apps/
Try a different SD card?
I had the same issue, and I think it was due to moving around the core files and configs while testing. I haven’t had the problem again since I set everything up properly now. In my case, it was odd but removing the "remaps" folder (RetroArch/config/remaps) somehow did the trick. Try not to copy or move files inside the RetroArch folder, as it seems pretty finicky now in that regard, at least in my experience.
Thanks guys. Managed to get it all working.
As september796 said, it's a case of being careful which files are copied over from a previous RA installation. Here's what worked for me in case it helps anyone else with similar issues:
1) With your SD card in your PC, backup your existing Retroarch folder somewhere on your PC
2) Delete all Retroarch files and folders from the SD card (SD\retroarch) (SD\wiiu\apps\retroarch.wubh)
3) Copy the latest Retroarch build onto the SD card and then put the SD card back into the Wii U
4) Fire up the Wii U and open Retroarch. This will generate a config file and allow you to test that the basic build is working
5) Power off the Wii U, remove the SD card and put it back into your PC
6) Copy any roms, savestates and remap files from your previous Retroarch folder to the new one on the SD card. DO NOT copy any cores (although you can copy savestates and remaps from the "cores" folder)
7) Put the SD card back into the Wii U, fire up Retroarch
Hopefully, everything should work fine. You might have to set some stuff up manually again but it should all at least work.
The only issue I'm having now is that I sometimes can't save/load core options files from within Retroarch. Not sure what's going wrong, but... at least the games are running and the savestates are working.
I do a bit of programming in my spare time, I'd be happy to help get Retroarch working properly in Aroma depending on what the issues are holding it back from a fully stable Aroma-ready release.