I Reported this a couple months ago, I remember doing a flight from AMS to CDG and if I'm not mistaken it doesn't only happen at VORs, I believe waypoints as well.
My Global subscription ended around the same time and flying without global i never encountered the problem again.
I recently reinstalled the sim and Bought Global and all is well so far too, haven't encountered it.
So try reinstalling the sim and see if that fixes it.
It happened on multiple versions, so can't be a "rereinstalling will fix!!!" problem, like I said, my flight plan was terrible and the game got confused