Yes, it's consistent, and it's usually the process icons that are the worst. I'm trying a few scenarios now to see if there's any specific pattern related to window size, project state, etc.
In general, though, I neatly stack all the process and shaded image icons towards the right-most side of the window before I save the project. If I close PI, then restart PI and open the project, as the icons are reloaded a number of them end up in random places, usually somewhere on the right-most side of the PI window, but not where I left them. As I mentioned, some of the shaded window icons are stacked on top of each other, making it hard to find them.
I'll try to put together a small project that demonstrates this.