How to Hide "Hidden Files"??

This is a question that has stumped AppleCare when I called them last week, and the "Geniuses" at my local AppleStore yesterday....So, throwing it out here. On upgrading my new 17" MBP last week to Snow Leopard I discovered the Finder was showing a lot of System files that normally are "hidden". IE: bin, cores, etc, mack kernal, tmp, usr, var. The regular way of dealing with these files is to make them "hidden" with a Terminal command, but that didn't work. I reinstalled Snow Leopard twice, that didn't work, the Genuis applied a Widget to hide the files, that didn't work either. Somehow the Snow Leopard installation has labelled these files as visible and will not allow Terminal to re-label them so that they go back to their proper "hidden" state.
I cannot with Snow Leopard find a way to "Archive and Reinstall" so that I could sort of shove aside the troubled system and put another clean one in place like we could with Leopard and previous OSX installations. So does anyone have any ideas what may have happened here and how I can address it without the painful solution of wiping the HD and reinstalling and re-registering everything like Photoshop, FCP, Lightroom, Aperture and a host of other software? Something I am trying to avoid. Thanks............

Peter Mullett wrote:
This is a question that has stumped AppleCare when I called them last week, and the "Geniuses" at my local AppleStore yesterday....So, throwing it out here. On upgrading my new 17" MBP last week to Snow Leopard I discovered the Finder was showing a lot of System files that normally are "hidden". IE: bin, cores, etc, mack kernal, tmp, usr, var. The regular way of dealing with these files is to make them "hidden" with a Terminal command,
which terminal command are you talking about? the regular fix is this
http://www.macosxhints.com/article.php?story=20071107023334449
it's for leopard but I believe it works for snow leopard too.
but that didn't work. I reinstalled Snow Leopard twice, that didn't work, the Genuis applied a Widget to hide the files, that didn't work either. Somehow the Snow Leopard installation has labelled these files as visible and will not allow Terminal to re-label them so that they go back to their proper "hidden" state.
I cannot with Snow Leopard find a way to "Archive and Reinstall" so that I could sort of shove aside the troubled system and put another clean one in place like we could with Leopard and previous OSX installations. So does anyone have any ideas what may have happened here and how I can address it without the painful solution of wiping the HD and reinstalling and re-registering everything like Photoshop, FCP, Lightroom, Aperture and a host of other software? Something I am trying to avoid. Thanks............

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