.DS_Store files are folder specific. Each folder gets one, and they are used for that folder no matter which user is logged in. A problem in a .DS_Store file would persist for any user, so it's not impossible that's the problem.
(Grelber you are going to love this — NOT
)
Yes but.. Not every folder gets a .DS_Store file. A DS_Store file is only created when the view for a particular folder or the location of the window on the desktop is modified. This is further confused by the view that is seen is inherited from the view in the highest level folder that is opened. For example if you open say the /User folder in column view and drill down to /User/youraccount/Library/Preferences everything will be displayed in column view set for the /User folder — even if the lower level folders have their own .DS_Store files and are set to open in another view. The same is true of List view and Cover Flow view. Icon view is the exception to this rule. In icon view each folder that is opened as you drill down through folder levels will be displayed according to the view setting in its unique .DS_Store file or lacking a .DS_Store file your default view setting. I suspect the reason Apple made the icon view an exception was to preserve some resemblance to the OS 9 behavior. This top down .DS_Store effect or the default effect that may be causing the behavior you are seeing with folders imported from OS 9.
Whether this helps your understanding of what is going on or adds further confusion, I don't know. Personally I long ago settled on Column view for everything which always presents a consistent viewpoint.
Jon has already mentioned OnyX, but TinkerTool System and Cocktail will also delete either individual .DS_Store files or optionally drill down through an entire folder hierarchy to delete all the included .DS_Store files.
