This might be linked to another issue, that of continuously 'fetching' admin permissions in the Get Info panel (see https://discussions.apple.com/thread/5171668?start=0&tstart=0). I had icon problems with all iterations of 10.8.x. In my case, for some folders such as ~/Documents (but not the Desktop), icon sizes (but not their placement) would reset to some default when I saved a document into these folders using 'Save as...' from an application. Deleting or restoring .DS_store or Finder preferences from a back up did not change this behaviour.
I did the following:
1. Repaired permissions using disk utility (did not fix the problem).
2. Typed "id" (without the quotes) at the command line in Terminal. In the output, Group 20 (staff) was not present.
3. Typed "sudo dscl . append /Groups/staff GroupMembership `whoami`" (again without the quotes) on the command line, and entered my password when prompted and rebooted (this did not fix the icon or the 'fetching' problem).
4. Rebooted into Repair Utilities mode (by holding the command and R keys). Mounted my HD using Disk Utility (it is Filevault encrypted), then opened Terminal from the Utilities menu and typed "resetpassword" at the prompt (again, no quotes). This does not reset your password, but opens an app. In this app, I selected the HD and select 'Reset Home Directory Permissions and ACLs' from the drop down menu at the bottom and clicked the Reset button. This reset permissions for my user account, see here. Then I rebooted normally (this fixed the 'fetching' problem, but not the icon problem).
5. Finally, I changed permissions for my ~/Documents folder (and all subfolders) using the Get Info panel by deleting the Staff permissions entirely, and changing the others to User (me): Read & Write; everyone: no access (this fixed the icon problem). This was done to match the existing permissions on my (unaffected) Desktop folder and has not affected usage of documents in these folders.
I haven't tested it, but step 5 on its own (deleting the 'fetching' permission, rather than 'staff') may resolve the problem with icon settings resetting or altering.
This is most likely a hangover from migrating my user account through several versions of OS X over the years (I've used OS X since 10.0). My current Mountain Lion user account was migrated from Snow Leopard.
Hope this is of use to someone!