I think I've found the solution:
You know when you first boot it up, if you played a GBA game the last time you played, then a quick message will appear saying, "Processing GBA save...", correct? Well, if you boot it up without the EZFlash, then the message will still appear, but since the save file is supposedly stored in the Slot 2 cart, and if you have something else in, then it will just overwrite the save file with blank data.
So basically, if you play a GBA game, make sure you put the 3in1 back inside of the DS before booting up the AceKard again.