Could you define say how you are arranging by name and what version of Mac OS X you are using?
in any version there are two things you can do. one don't use global settings in command+J. for some reason on my computer the folder will be scrambled until I go to View -> Arrange -> Name after I have deleted the DS_Store files within the folder with Cocktail.
http://www.macupdate.com/info.php/id/10909
The second one is use something like Path Finder to view your files and apps
http://www.macupdate.com/info.php/id/6371
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I really wish Apple would make up their mind. the finder is between a file browser and a spatial system of viewing files. in one you have a list of things like a global arrangement by say name or something and in the other you have folders and you put things there and there they should stay in the order and spot you put it.
personally I prefer the finder to be a file browser or at least have a way to "clean" the system of any and all user defined placement that will translate to CDs and over the network.