Ugh, my N3DS XL is reminding me about why I stopped playing Animal Crossing in the first place.
If I shut the screen too hard, there's a chance of it turning the entire system off, something with the battery it seems. Naturally it resets the system clock and the game gets mad at me every time I boot it up again. For most games it is a minor annoyance where you just have to make sure you're all saved up before shutting the device, but in Animal Crossing it is sheer brutality if you're trying to get things done.
I rigged up a plastic wedge that fits into the gap of the battery to help hold it in place, and then folds over to be held in place once I screw the shell back on, and so far this morning it hasn't been really giving me any crap, but it can be really demoralizing if it keeps up. Here's hoping it works, I've been looking forward to getting back into the game.