This bug has been opened here: http://bugzilla.ubuntu.com/show_bug.cgi?id=17204

"Despite having Auto Arrange unchecked, the Nautilus desktop icons always reset
their positions when I log in. Always, they're being reset to the position that
they would be in if Auto Arrange was enabled, for some reason.
...
> Thanks for your bug. What version of Ubuntu do you use. Are they aligned on the
grid or autoarranged like if you picked the "sort by name" option?
...
Oh, sorry. Using Breezy 5.10 RC, and they are autoarranged if I select "Sort by
name". What's odd about this is that this never happened until the latest round
of updates in the last week or two. Before that, the icons always stay put.
...
Ah, i misinterpreted your question. I menat to say that they are aligned on the
grid as if I had selected Auto Arrange, not Sort by name.
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| Could you attach a screenshot of this behaviour?
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I have this problem too.  It is especially evident if you place icons on the
right side of the screen.  When you log in, they are either half-way off the
right edge of the screen, or they are an inch or so to the left of the edge (but
neither position is where I put them).  This problem began a week or so before
Breezy was released, and continues in the released version of Breezy (even with
a fresh install).  This bug wasn't in Hoary, nor was it in the early preleases
of Breezy.
....
http://bugzilla.ubuntu.com/attachment.cgi?id=4784
Before logging out screeshot

Before screen. USB drive and Trash bin icons placed where I want them. Note
"Keep Aligned" is uncheck. The bug only affects them; if you have your desktop
as the Home folder (as I do, with those other folder shown there), any contents
from there aren't affected.
...
http://bugzilla.ubuntu.com/attachment.cgi?id=4785
After logging back in screen

After logging out, then back in. Note the USB drive and Trash icons are aligned
as if Keep Aligned had been enabled. Rick Wood is right as in this problem
didn't crop up until about a week until Breeezy was final; it had been working
just fine in Breezy before then and in Hoary.