Font book not disabling / deactivating fonts

Most of my fonts (1000+) are currently disabled in Font Book, but they still show up in the font menus in the applications I run (Photoshop, Adium, Omnigraffle, Mail.app, etc.).
Why don't my applications just reflect the list of fonts I have enabled in Font Book?
Possibly related: After I upgraded from Tiger to Leopard, all of my fonts were enabled. I subsequently went into Font Book and disabled most of them (which is how I had things in Tiger).

I posted this below, but never had any replies or answers, I have since spoke to someone at the apple store who says:
I should not have them in my user/library/fonts, so now I only have them in HD/library/fonts.
My font book even after being cleared out still thinks and shows my old font history.
Last night my fonts were showing in Illustrator/PS/Indesign but now only shows a basic selection.
Was also told that I should not be running CS2 on my intel based MacBook Pro yet CS3 is not yet ready for Leopard.
I am just finding that my new MacBook Pro whilst fast and sexy seems to have moved away from the logic of old, maybe I am stuck in the past but my working day is greatly increase and eaten into due to clashing software and font problems.
Hi,
I recently got a Mac Book Pro with Leopard and transferred all my Files etc across when doing this I copied my Fonts from my Old G4 to my Mac book Pro and it does not recognise them and will not load them into Font Book, it always says bad font detected or will not validate them!
Obviously this is either a major oversight by myself or apples they work fine on 0S9 and on OSX but not with Leopard, can anyone help as these fonts cost alot of money!
I have also now been to a friend who is still on 0S X and copied them from my OS 9 G4 to a CD then tried them on his machine and hey presto they worked, so I then got him to copy them to a CD thinking I would then be able to make the step up again, but no I still can not access my fonts, Im getting stressed now because I am wasting time and energy on forums and asking friends and trying things, I have a deadline for a Design/Website which relies on this Font and can not get the fonts to work, Macs are meant to be a designers best friend??? I m really having trouble finding the patience with Leopard and it seems things have not been thought out, any one else had this problem or Is the answer starring me in the face, go back to OS X ??? Please Help a slowly depreciating MAC fan !
Thanks

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Robin --
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http://discussions.apple.com/thread.jspa?messageID=607630&#607630

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Kurt Lang wrote:
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~Bee, (sorry for delay in replying)
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Font book not disabling / deactivating fonts

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