Citra Reports (Falsely) that .3ds File is Encrypted

[phoria]

Issue:
I dumped my own .3ds file and the corresponding .CIX file to apply the patch to the ROM, and rebuilt the .3ds file after doing so. After attempting to load it in Citra, it stated that the file was encrypted. After copying the Patched .3ds file to my SD card and trying to decrypt it in GM9, it stated that the file was not encrypted. Any ideas?

System Information
* Operating System: Windows 10
* CPU: Intel i-7700k
* GPU: Nvidia GTX 1080
* Citra Version (found in title bar): HEAD-9fd26db
* Game: Pokemon Moon
* Screenshot of Issue (include the full Citra window including titlebar): http://i.imgur.com/b6oEoRZ.png

Log:
https://pastebin.com/PPcLW9Qd

[Leo121]

Changing this to general tag as rom hacking does not belong to support. There's a tutorial for updating ROMs here. Make sure to follow it.

[phoria]

I've gone through this process a number of times without issue. The file behaves as it should on an actual 3DS. To me it certainly seems as though this is an issue on Citra's side.

[Leo121]

Make sure the ROM is dumped decrypted. I tried updating my Sun ROM to v1.2 and it works with Nightly - 22e7402 and Bleeding Edge - 2b0f59f. Try doing it over from scratch.

[phoria]

Huh. The same dump works on a previous Nightly Build (cf15b65) but not on the Bleeding Edge build I was using.