Gateshark and NTR use different parts of the memory, but yes, you are correct.Gate shark works so it's an issue with the 3ds rebooting
When the 3DS reboots, it seems to clear NTR which is why it won't ever work on O3DS.
NTR's development was terminated, and there is no publicly available source for it meaning someone else can't just pick up where the developer left off and continue improving it.