Font book or CS2 font problem?

I am using a mac Pro, running OS 10.4.11, w/ CS2. I am having a problem with either font book or CS2. Certain fonts are not viewing correctly when I use them in CS2 programs. I get a font error when I open the file, and when I try to fix the font by choosing the same name again, the font appears as another font entirely (in fact after I closed and reopened everything the font it substituted changed, and if I choose italic it changes fonts again). I do not know if the issue is with font book or CS2, but I have installed around 1500 fonts, and have had some other minor issues when I open files in Adobe programs, with fonts not showing up even though they are installed and enabled. I fix that problem by disabling the font and then re-enabling it and it then shows up in the font list.
So after all that, my question is what should I do? Should I reinstall CS2? Or is the problem more likely cause by font book?
Thanks

Font Book is an inadequate font manager made by Apple for managing the few meger fonts Apple includes with the system.
FAP is a robust font manager made for professionals with thousands of fonts

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