Turns out, the memory was perfectly fine!

-=-=-

The issues in the level builder were..

1) Drawing thousands of pixels overwhelmed the poor little 3DS to the point where it started throwing oodles of errors. (Due to the lazy way I'm currently drawing pixels. This should be fixed in the future, hopefully!!)
and
2) Because the drawing is scaled down on the 3DS, the thinner paths weren't showing up.

So, it was all my own drawing code's fault!
I've reduced the sprite-limit for the 3DS code to something where it no longer freaks out.

Here's the generator's output on both the PC version and the 3DS one.





Gudgud!!!