If it was smaller, it wouldn't be writing the full save. In that case the check sums would be bad and would restart the game.
Since that's not the case, I don't know.
First, make sure you're using the latest firmware update.
Then,
What save size does the program report?
If you backup the save that starts a new game, and open it in Pokegen, does it work?
http://projectpokemon.org/forums/showthread.php?16601-NDS-How-to-Backup-Restore-your-retail-cartridge-save-file-for-DS-games
I recommend the NDS Backup Adapter Plus.
A friend of mine pointed out that it's made for little children who would easily break a 3DS and would get headaches from the 3D.
Still looks uncomfortable to hold.