I just tried the latest version and yes, it now works perfectly with the remapped game, but it doesn't work for the other games (c-stick not remapped).
Here's the issue visualized:
A = c-stick remapped software
B = c-stick not remmaped software
A > B Works
B > A Works
A > B > A Works
A > B > A > B Doesn't work
I couldn't go further as the console freezes when trying to get back to the Home Menu.
I've repeated all the steps above. Now ZL, ZR and the c-stick work, but ZL and ZR aren't holding pressure (it's like they're activating and deactivating continuously when pressed).
Seems to be random, hopefully it's fixable! Keep up the good work, patch after patch