Cura 2.5 definitely handles positioning differently from 2.4. Since Cura 2.5, CuraEngine is using multi-threading to speed up the process. The engine generates multiple layers at the same time. The major disadvantage of this is that the engine doesn't know where the previous layer ended in order to get the point on the inner walls closest to the previous print head location. Instead the engine starts each layer closest to the Layer Start Location.
A workaround for your situation is to set the Layer Start X and Layer Start Y to the same values as the Seam X and Seam Y.
I don't think this is a problem for most prints, since most prints use infill, so the starting point of the inner walls is already closest to the last infill line, rather than the end of the outer wall on the previous layer in both Cura 2.4 and 2.5. Moreover, we think that having the location of the seam of the inner walls at a different location as the seam of the outer wall could help strength prints and reduce the size of the z seam which is visible on the outside.
Love to hear your thoughts.