Resolving duplicates doesn't fix my broken font

Question

I'm new here, I admit, but I can't find anything on this one in searching, so I'll start from scratch. I'm happy to be redirected or moved, though, as this problem goes beyond just Safari (3.1.2). I used to understand computers a lot better, before all this GUI stuff kicked in, and now I've forgotten what little I ever knew. There may be stupidity ahead...
What does it mean when "resolve duplicates" doesn't resolve the duplicates, and the fonts still don't work? They don't display properly and the dot remains in the Font Book saying there are duplicates.
One of my fonts is broken - I think it's Arial, even though I've removed the font family. The letters have breaks in them, and it becomes very difficult to read. I've had this problem before and fixed it by using the "resolve duplicates" button in the Font Book, but this time it said that particular font didn't have any duplicates - there was no dot after it in the Font Book listing. I hit "resolve duplicates" anyway. Didn't help. I tried just disabling the font. Didn't help. I finally removed the font. Didn't help. And yes, all steps were followed by rebooting. Validated fonts, no problems found.
I have tried resolving duplicates of other fonts, and it doesn't actually resolve them - the dot after them in the Font Book remains. So I disabled all of those, too. More rebooting, more not helping. I downloaded FontNuke and used that to nuke my caches - again, didn't help.
Google is still using Arial somehow, and is often illegible, but not consistently so, and the same for many web pages. Mail (2.1.3) is also using it somehow, and again is often illegible but not consistently. I've reached a stage where I think I need a walkthrough to untangle this, and can't find anything. Lugging my iMac into a Genius Bar is deeply unappealing, but if that's what I need, I guess I'll do it. Would love to hear otherwise.
Some related queries: when I download fonts and install them, can I then delete the stuff in the download folder? I coralled 'em all in a different folder till I find out, and then even moved 'em to Trash, which I'm now scared to empty in case it means losing all my fonts.
Please help! Please please please!

Answer 1

I know I had the problem once before. I highlighted the font with the black dot, hit the "resolve duplicates" option in the menu, and poof, dot gone, problem fixed, happiness and rejoicing. Now, though, bunches of fonts have the dot. Hitting the resolve button sometimes removes the dot till I reboot, then the dot's back. Heck, disabling the font also does nothing - when I reboot, they're all enabled again.
I have in fact tried to delete some fonts that it said had duplicates, only to find there was only one copy of them, and try as I might I couldn't find the duplicates. I would like to know why this "resolve duplicates" thing sometimes works, and sometimes doesn't. And oh yes - the Arial font is still messed up in NeoOffice, which is just another reason for not using NeoOffice, for me! But it's only messed up there - in other programs, it's working fine.