Hey, I've been having the exact same problem here on my iPhone 5, jb 6.1iOS. Initially upon respring out of Cydia it was working great then I immediately went into settings and as soon as I altered some settings for Aquaboard I noticed that the wallpaper was offset just as you mentioned. I hope it's just an error in the app and not an anti piracy tool. That would just make things difficult and confusing.
Here's to a solution/update,
-Austin