I also have had this problem and it's made me cry because I'll spend hours of time and effort to make the terrain paint look nice, only to notice that it's slightly shifted, but here's some things I noticed that might help those who will (hopefully) fix this bug. It happens to me when I either a) place a build from the gallery on a lot that it wasn't built on, b) save my own build to my library and try to place it on a different lot than I originally built it on, or c) rotate a build any degrees (the paint will look nice only on the original angle). Recently I was updating the onsen on Mt. Komorebi, and I wanted to add some terrain paint without the snow getting in my way, but it always snows up there even in build mode, so I saved the build to my library, placed it on a different lot that doesn't have snow on it, painted my terrain, and when I replaced the build, it was backwards. It was only after I rotated it that the terrain paint shifted. I tried going back to temporary lot where I painted the terrain and to other lots of the same and different sizes, but the terrain paint always shifts. I wouldn't mind moving the building and objects to match the new terrain paint location, but because of how slight the shift is (~1/4 tile diagonally), it's impossible to match the building back up. I know this post is old but I really hope my reply gives it some attention!
