That is the most common cause of such issues.
You may always want to try Stardock's new application Fences, which is currently a free (stable) beta. It works around such Windows quirks and adds some nice features as well.
For some reason, when I change th location of the desktop icons, upon logging back in, the icons are reset to an "auto arrange" looking formation. The auto arrange box is not checked, the align to grid is.