System fonts not showing in Font Book

I am using Font Agent Pro as a font manager and am wondering if there's a conflict with it and Apple's Font Book. I cannot get the system fonts to show up in Font Book and, hence, those (System) fonts don't show in Apple apps, e.g., Safari, Grapher, Text Edit, etc., etc.
The only way I can get the system fonts to show in apple apps it to drag the System>Library>Fonts folder to the "Collection" column onto the "Computer" collection. This is fine, but it copies the System fonts to the ComputerName>Library>Fonts folder.
I've tried for hours to get the System fonts to show in Font Book and do it without the System fonts being copied to the Library or User folder, i.e., I want the System fonts to stay in the System fonts folder only.
If I boot into another partition and bring up Font Book everything works as I would expect, and Font Agent Pro is not installed on that partition...
Any Ideas?
TIA,
Geoff
Quicksilver 933, PB 15" 1.67 Superdrive Mac OS X (10.3.9)

Hi PS1,
I am using Font Agent Pro as a font manager and am wondering if there's a conflict with it and Apple's Font Book.
Yes, in a sense. If you always open and close your fonts through FAP's interface, then it's no problem leaving Font Book on your Mac. It will simply sit there and take up a small amount of disk space.
That said, it's still a nuisance having more than one font manager on your computer at a time. Say you disable all of the fonts in Font Book that you can. Assuming the fonts are still in the /Library/Fonts/ folder, you then turn them on and off with FAP. The problem then is which orders are the applications going to believe? Are the fonts active, according to FAP? Or inactive, according to Font Book?
Also, if you double click on any font to quick activate it, both FAP and Font Book will activate the font. So you will find yourself confused fairly often when you deactivate the font in FAP, but they still keep showing up in your applications as active. That would be because Font Book is still holding it open.
So if FAP is going to be your main font manager, then copy Font Book off to another disk for safe keeping (so you don't have to use Pacifist or an OS install to get it back on your system if you need, or want to), and then remove it from your hard drive.
Definitely don't remove the /System/Library/Fonts/ folder! If you remove Lucida Grande from its default location in any way, you will lose control of your desktop. The only way I can think that Taavi managed to accomplish this was moving files around booted to an external drive, or from another Mac via FireWire Target Mode. It's impossible to do on the same drive your booted to. You'll lose control of the desktop every time if you remove Lucida Grande. Although Taavi may have made his/her copy to the /Library/Fonts/ folder. That at least would still leave an active copy of Lucida Grande somewhere, but I highly recommend against that sort of handling of the system fonts.

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