Thank you for your answer. I had the exact same issue, dual desktop.ini files named the same name. By going to folder options and setting the two options to display system and hidden files, I found 2 desktop.ini files on my desktop, removed them and this
fixed the problem.
After initially going through several frustrating re-arrangements of the icons, attempts to set them back and having them a tossed mess on the next reboot, this fixed the problem. I might also add that my loss of icon arrangement and double desktop.ini
appeared right after I re-sized the partition containing Windows 7. So this might be a good final check point after resizing a partition that contains Windows 7, to set visible the hidden and system files and delete all occurrences of desktop.ini. (Not
sure what all the desktop.ini files are for - Win 7 seems infatuated with them :-). I deleted both of the ones on the main desktop and it didn't seem to cause any harm and neither have reappeared but my icons are staying positioned now (with AutoArange NOT
checked and Allign to Grid CHECKED). Not sure if any of this is related to my NVIDA dual monitors or not, but the problem is fixed for the moment.