I want to apologize for I hadn't describe it clearly.
At the beginning we thought your shape file is not the same projection with your geotiff file, so we only set projection to the shape file(it contains the prj file). That's why I mentioned the two layer cannot cover.
And after that when our developer implement the workaround, they ignore the projection, so you are right, if assign projection the jump appears obvious.
Just like I mentioned, it's hard totally fix the not match between raster and vector layer, so the project magnify the not match result, that's why we watch the jump after reproject.
I will ask our developer to research it and see how to provide a solution or workaround.
Please wait my update.