I'm having this problem too.
I have a bunch of files and folders in my home folder, arranged manually. They get messed up randomly by OS X Lion Finder.
the triggering cause seems to be when I Save a file in some app, via the Save/Save-As dialog box that pops up.
first, here's my setup:
My home folder's view options (Cmd-J) are set to:
- always open in icon view
- browse in icon view UNchecked
- arrange by None (i.e. manually arranged)
- snap to grid
- icon size 32x32
normally every time I open my home folder, all the icons are just where I left them (as they've always been for every other version of Mac OS I've used!)
now, here's how to reproduce the problem, at least in my case:
- open home folder in icon view - all icons are neatly arranged where I put them manually
- select all icons, do a View/Clean up selection, just to make sure they're all on-grid
- close the home folder
- open Mail app
- choose an email with an attachment
- save the attachment to the home folder, via the dialog box that pops up
- go back to the Finder, open the home folder
- now all the icons are messed up, many moved to different/random locations, many of them off grid, some of them overlapping other icons
perhaps others experience this problem can confirm if the Save dialog box is the triggering action in their case.
definitely a bug in Lion. very annoying.