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I had the same problem.
Hey, it's been a while since this topic was discussed. Did you find a solution to the problem. I fixed the issue in my project. I found that the 9-patch on my layer that had the Seams to "overlay" caused the issue. I hope this helps.
This issue persisted with me through the life of my project. I was disabling force own texture as a way to work around it, but it was never 100% perfect. I had been recently working on my inventory and noticed that when I was copy and pasting multiple 9-patches in rows and columns, the objects would look as if they were on a different layer x.+400, y.+400 offset. Knowing where the actual object really was, I continued creating my inventory menu. Messing with transparency, I noticed that the seams needed switching. After the first two 9-patches next to each other were set to "Exact" seams, they were no longer offset in a different spot. Repeat for (loop) each 9 patch and it's been working flawless. The objects in close proximity to the 9 patches were no longer skewed.