Ok so I've tried to solve this for days now, and I didn't imagine such a trivial problem could be so impossible.
So I'm dual booting Win 7 and Karmic Koala, and cause I do use them in a equal rate I'm using 1 ntfs partition as a storage drive for both Operating systems.
So I used pysdm to auto mount my storage partition at boot, and cause I use desktop icons (shortcut,links...whatever) I've linked some of my folders to the desktop via drag and drop and "link here" option.
My problems is that every time I reboot ubuntu those icons rearrange to some default position no matter where I put them on my desktop, and in some occasions they overlap.
So can pleas someone help cause I'm going mad here. I've posted on so many forums and no one seems to answer. By now if someone just told me that it can't be fixed, it would be great.
Shed some light!

only gui option I know is right-click somewhere on desktop
and un-check "Keep Aligned"
?

See if you have gconf-editor installed (if you don't, install it). Run it and look under apps/nautilus/icon_view or apps/nautilus/list_view. Maybe if you play with the options there you can stop gnome from rearranging your icons. On my system all the options are unchecked and I think it's what you want to have too.