Often it's due to a resolution change by some gaming software or merely booting to Safe Mode, which invokes the VGA driver.. Sometimes it can be caused by malware.
I use a handy little tool that restores the order when it gets scrambled. IconSaver
There are two versions, one is totally freeware while the other is shareware. I have used the free version for years and wouldn't be without it. In getting the link for you I find that I may want to try the shareware version now.