I found your post because I am looking for a solution to a similar problem. My icons are not quite as scrambled as yours, but Windows installed 29,361 updates today and after that, all the icons were neatly arranged in a compact array at the left side of the screen, with those for spreadsheet programs, anti-virus, browsers, and various junk all randomly thrown together. So, I organized them into categories again, hoping for the best, but it may not be worth the effort if it won't last. So, I will be watching this thread to see if anyone suggests a way to explain to the demon in the machine that it should leave them alone. Surely in a proper, well-run world the user would be able to arrange the icons according to personal preference, but maybe not in the real world that we live in.
It's a little like working with spreadsheet programs, where you have stuff on various pages, and when you go from, e.g., A to B and then back to A, the page is moved around randomly so you don't see the data you were working with on that page until you navigate back to it. Or Windows Exploder, where you click on a sub-folder and the whole column moves up or down so that the file you are looking for is near or past the bottom of the screen and you have to explain that you want it back up where you can see it. I am fairly sure that all of these bugs were intended as features, but the software writers can't know enough about what the many users are going to want; and the results I have seen are so bad that I don't think the system is even doing what the writer intended; no human could be that dumb, it takes a recreant demon in the machine to be as mean as that :-)