I'm guessing that your problem with the 2nd Palace is somewhat like the problems that I posted images of in the thread above. I have images for other games in other threads, but I think they're in the 3DN threads, so I didn't dig them up.
I don't think it's a bug with 3DNes or it can really be blamed on the way Zelda II was programmed. I think that this is just because 3DNes is still growing and these issues are just challenges that geod is working to overcome in future versions.
A few of us have already suggested the ability to select a group image and spit it up and manually re-group and re-shape it. We have not heard back from geod if this will be possible yet, but this would eliminate this issue if the user had more control to fine tune these things.
I wouldn't play the game again just to get a screenshot until save states are implemented. It wouldn't take a ton of time for you to get back there now that you've done a ton of the 3DN work, but it's not worth it just to make an image IMO. You'd have to do it again when the savestates were included.