Ok, this is not a "fix" - only Apple can provide that. However, I have discovered a viable work-around that doesn't stop the windows re-arranging themselves in the first place, but makes it a whole lot quicker and easier to restore all your windows to exactly the way you had them before the problem occurs.
There is a $15 shareware program called Finder Window Manager (FWM) that has been around for a while. What it does is let you create any number of "window sets" and them restore them from a drop-down menu should any windows in the set become re-arranged for any reason.
Once the program is running (and I recommend making it a "Login item") you just have to set your windows to the exact way you want to view them, with the proviso that you cannot close any of them until they are all ready - so you may have a very cluttered desktop while you're conducting this first step. Once all the windows are ready, you save them as a 'set', which is then listed in FWM's drop-down menu in the Finder menu bar.
If Lion re-sets any windows in the relevant set, you just go to the drop-down menu and select to restore the set. All the windows in that set are re-opened at once and configured in the exact way you saved them. Although you are then left with all your restored windows open at once, I just press command-w as many times as required to close them all, which only takes a few seconds.
And there you have it. Instead of painstakingly re-setting all your windows manually, you have the peace of mind that they are always saved and ready to restore within a few seconds.
If you have a very large number of windows that Lion re-arranges, you can create multiple sets which can be restored separately fom the FWM drop-down menu. For example, I have a set that fixes all my folders in the root directory of my hard drive, and a second set to restore folders in my User account and all the folders on my desktop, which Lion seems to re-arrange more frequently than the others.
Note that because this program fixes folder views by restoring and re-opening all the windows, it will not fix the desktop icon re-arrangement bug. For that problem there is a program called DIM (version 2.0.2) which works perfectly for me.
Lastly, FWM seems to have a feature that can monitor all your open windows in real-time and keep them fixed to the view settings that you have saved.
Well, these two programs have taken the pain out of the desktop and folder re-arrangement bug and have made life tolerable for me while I wait for Apple to fix the underlying problems in the Finder.
I hope this advice is helpful. 😀