The background issue is solved, but the game is still unplayable because you can't exit to the world map.
About the fix for the backgrounds, is it supposed to make the image shift everytime the background changes, such as selecting different characters in the menu? I can see exactly where it shifts on the screen(much more noticable in higher resolutions), such as a transparent vertical line and a colored vertical line on the left and right edges of the screen, respectively, as well as 13 evenly spaced transparent horizontal lines. It's like this in all of the games that were affected(Atelier Iris 1-3, Ar Tonelico 1-2, Mana Khemia 1), and while it's a very minor shift, it can get very annoying in scenes where it shifts every second, the most noticable one being dualstalls in AT2.
I'm not sure if it's like that because that's the only way to fix the issue or because of a bug, so I thought I'd mention it just to be safe. If it has to be like that then that's fine since it's definitely an improvement from before.
Also, there are still bugs left in AT and AT2 that are mentioned in their respective threads(black squares around faces during conversations, falling through the floor when running up against treasure chests with EE rounding set to chop/zero, world map issues), but the floor one probably doesn't count as a bug since it's an advanced option issue, and the rest seem to be GSDX related, so should I make another thread in the plugin section to replace the ones you locked, or should I post about them in the GSDX thread?