That might be the case. I did have a version with an earlier patch installed several months ago. Thing is, I've wiped and even formatted the SD card between then and now. Another note is that I've tried installing the unpatched cia, and everything is in japanese, so I'm skeptical of something overwriting the files. There's certainly no trace of anything in the 3ds data management. Is there something I should look for on the sd card?
Edit: I did some more investigating and extracted both the patched and unpatched cias to compare them with the patch files. It seems the patch files for supports are indeed being copied into the cia, but you can see the original files with the japanese filenames are also present. This now leads me to believe that even though the patch has been applied, the game is ignoring those files in favor of the originals. Could that be what's happening?