Loading the same crystaltruncated.sav file I posted before produces the error "Gen 2 Location 126 not recognized."
Opening a gen 2 save shows a window with "Pokedex" listed as "Pok..." This may be because the button is shorter than the other buttons.
Opening a file starts in the home directory, not in the current directory. You could argue this, however, opening a second file starts in the home directory again and not in the directory the first file was opened from, which is harder to justify.
Suggestion: When showing the boxes, show the boxes with the same number of rows and columns as the original. For instance, Pokemon Emerald's boxes contain 5 rows of 6 Pokemon each. You changed that in the editor to 3 columns of 10 each, where a row in the game corresponds to part of a column in the editor, making it hard to see what the box layout will be. Using 5 rows of 6 will be uglier but much more useful. Also, I still suggest showing the box name used in the game.
Loading the attached Emerald save produces numerous errors about moves, origin games, species, items, and symbols not being recognized. Some of them have suspiciously large numbers (move 58927?). The save file includes Pokemon that have been migrated from and Colosseum (but not anything migrated from fire red/leaf green).
Copying a Pokemon doesn't set the Pokedex entry as seen and caught. There's a "Max" which sets everything to seen and caught, but there should be something which sets only the Pokemon that are actually in your party or boxes.
POKEMON_EMER_BPEE00.sav