BernardoGiordano has released a new version of his savegame manager for the Nintendo 3DS:

3DS: What's new

Fixed compatibility with lots of games. Titles that caused troubles like Scribblenauts, Shin Megami Tensei or Paper Mario are now fully supported by Checkpoint.
Fixed compatibility with "counterfeit" DS cartridges.
Turned out they just were undocumented cartridges, which now are fully compatible with Checkpoint.
Fixed issue causing Checkpoint to error when loading garbage titles installed into your nand.
Fixed crashes happening when the cursor was moved to a location without titles.
Fixed crashes happening when exiting target title after backup navigation.
Fixed crashes caused by text rendering issues (thanks @pcbeard).
Code cleanup and multiple minor fixes.