In my case the problem has gone away with OS X 10.8.3 and 10.8.4. So far, so good since April 2013:
Mac mini 2012 (2.6GHz Quad-Core Intel Core i7 - 1TB Fusion Drive combining 128GB SSD with 1TB 5400 RPM HD)
2 units of iMac 21.5-inch 2012 (1920x1080) 3.1 GHz (Turbo Boost to 3.9 GHz) Intel Core i7 (4 cores; 8 threads) 16 GB RAM
I believe this issue dedepends on the graphic card of the Mac.
I'm having the same issue on 10.8.5. Everytime I switch profile it jumbles up all my nice neat folders placed how I would like them, into random crazy places. It's like it wants me to be messy!!
This is so frustrating.
I tried ditching the com.apple.desktop.plist on both profiles but it just doesn't work.
Also tried using an old app called DIM but that doesn't work either.
It's got so bad that it's now placing items on top of one another.
I've got it set to "None"
How can I get them to stay put?....Please someone?
Totally cheesed off with this.
10.9 finaly solved almost all these icon problems.
They clearly changes the way they manage icons.
Still not perfect I think but not big frequent trouble anymore.
In the worst case everything is coming back after restart.
Everything began to go wrong in June 2008 with Snow Leopard 10.6.
Apple has never solved the problem.
Maverick 10.9 is acceptable, but works less well than Leopard 10.5 from this point of view, this is pathetic.