New
#11
There might also be a resolution decrease happening somewhere from shutdown to restart.. (and then switching back to normal)
Try this:
Fix your icons the way you want them, and then change your resolution to a lower one. Windows places icons that don't fit the current resolution to an alignment of its own.
Do this and see if the icons get messed just the way they do when this occurs to you.
If so, consider updating your graphics driver, disabling your graphics driver's startup application (the ones sitting on the tray) or check for startup programs that might mess with your resolution and disabled them.
Just a thought.