Invisible files all visible

After running cocktail for my regular maintenance last night, all my invisible files are now visible.
I have logged out and logged into another account and my other user accounts are fine.
I have repaired and verified my permissions, restarted, logged in and out.
Can anyone shed any light on this and how I make these files invisible again?
(Dual G5 1.8 tower)

I have found the answer after some digging in the support forums.
This question is answered though some confusion remains on what happened!

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    Note: The information provided in the link(s) above is freely available. However, because I own The X Lab™, a commercial Web site to which some of these links point, the Apple Discussions Terms of Use require I include the following disclosure statement with this post:
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