Hello,
I am having the same issue with YMML and EFRO.
Both two very different airports and the ILS is offset from the centre of the runway.
As this is a very old post originally, I was hoping that there would be some sort of solution.
I too had to reload Windows (with Version 11 though) and have completed this in a completely vanilla installation of MSFS2020 and immediately got the offset on Runway 16 and YMML. Incidentally I was flying the stock King Air and also the FBW A320.
I never had this issue until recently. The runways always lined up.
Does anyone know how to fix this?