I had a similar issue with a Pokemon X rom I actually just tried to start editing. I know this post is what, closer to 3 years old now, and I'm using a different version of PK3DS, but I'm just trying to use a different file. Considering though that you have a rom with changes on it already, I have no clue. I'm just a user, and considering how long it's been since you've posted this, you've probably troubleshooted it further than I have in the past hour. But, nonetheless, I hope your file finally got extracted eventually. I'm just glad knowing that at least someone out there got a similar issue and it wasn't just me. Was this comment useless? Yeah. But, if you're slowly going insane about this problem that no one else has said they've had (which I doubt) but just in case, know that you're not alone. Even with different versions of PK3DS. Then again, I've had similar issues with other editing tools on my computer (Specifically looking at you, gen 5 and 3) so maybe it's just a me problem, I don't know. You probably wanted a response from somebody who knows what they're doing. Main problem that I can see is that the data that's supposed to be of the same memory size (the array) isn't. Which I'm pretty sure just comes back to the problem being the actual rom itself (as this would mean that something in the rom is too big) at least I think. You would really need knowledge from someone who knows more than the most basic of basics about computer stuff.