Invisible files are visible

I ran disk utility the other day and it couldn't complete due to errors. Since then I ran applejack which ran to completion. After that disk utility will run to completion with no errors. My issue is that now the invisible files show up (.DS_store). Also, the icons in the preferences window have changed. Most of them now look like a light switch with the upper right corner folded down and the original icon shows up in a miniature size on the lower left corner. What gives?
Thanks

Follow the instructions here and here.
(48511)

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