with some stories (Gaia, Brent Land) the game freezes during the optimization. so i turned optimization off for Gaia, but then when i reach a particular spot, the game freezes everytime. you'll find this spot by starting at savepoint at X=1055, Y=1003 and jumping the next two screens upwards.
i tried to avoid both problems on several flash-cards (cyclo evolution, m3i zero, m3simply) and also tried the compatibility version with sound deactivated.
hopefully there is something that i or you can do about it
and btw: totally love the game & totally love playing it on my ds. so thanks for your awesome work
/edit:
another problem: maybe the jumping height is a little bit less than in the original game. In Fredrik Andersson's "Core", starting from savepoint at X=992, Y=1015 (after collecting the higher jumping ability on the left), going down and the next screen right, you cannot pass the gap (see attached picture).