At first I thought it was because of the announced hack checks from doing Ratings Battles/Competition with a modified save file, but this problem came back today. I believe it came from using PKHaX, but the first time, it could've been PKHex. I used the latest commit at the time, a couple days ago. On the first go, it might've been when I made it so a hacked Deoxys (with illegal ability and moves) got Pokerus. Editing that kind of hacked pokemon on PKHex reverts its ability back to a legal one. After that and regular genning, whenever I go to the PC, the screens go black. Music still plays, controls don't work, the only way to exit is to force shut down or take out the cartridge. Note: this is from a Gateway ROM, I bet the same would happen on the retail carts.
So the second time today, I know for sure tinkering on PKHaX did this. I put an illegal ability on the Deoxys, and proceeded on with the game. Then I go to the PC, black screens. Since PKHax is just renamed PKHex, and this specific version is from the commit before the brand new one, I think it causes the save to be damaged when playing around with illegal pokemon. In comparison, on the latest exe version of PKHex (4/4/15), renamed to PKHax, tinkered again, no problems at all.