Fonts showing up in Font Book, but not in other apps

Question

This morning, while rummaging through Font Book for something new to use, I discovered that some of my (large) collection of fonts did not show up in various programs... meaning I never think of using them unless I'm actually rummaging through Font Book.
I got onto the Apple support forums and looked at why this might be. I discovered that some of my fonts, for various reasons, were only in the "User" folder, while some that were listed in "All Fonts" were NOT showing up in the User folder. Cleaning this up seemed like a good place to start. I quit Font Book and all other programs, went to /Library/Fonts and ~/Library/Fonts, and moved all the fonts in the User folder into the All folder, as suggested on some answers here. (In addition I changed my Font Book prefs so that new additions in the future will not go to the User folder, but to the main folder and be usable to all.)
Then, also following answers here,
—I did a Safe Mode reboot
—rebooted again out of Safe Mode
—removed font cache files through Terminal
—and finally checked Font Book.
The screen shot above shows that all fonts are under "All Fonts" now, instead of some showing up only under All and some, oddly, only under User, as it was before I started the cleanup. Nice and neat. There is no User folder anymore, and I assume that is because it has no contents—User gets what All gets. Seemed like everything worked.
So I opened one of the programs I use to take notes (Microsoft Entourage), just for a quick check...
... and discovered that some fonts which *have* always been usable, are now not showing up. (On the plus side, however, some of those fonts which had been hidden to me—ones that I discovered in my morning rummage—are showing up, so half of what I was aiming for is working.)
I read a few more support forum posts, and saw that some folks have success when they remove the fontbook .plist. So I did this as well, and checked everything again.
Font Book itself is still nice and neat, and appears to be complete, but Entourage and TextEdit, which I chose to be representatives of how this font cleanup is working in real programs, still do not show all my fonts. And stranger still, though most of their problems are the same, each of the programs also has different fonts which are or aren't showing up!! For instance: Aviano Slab, shown highlighted in the screenshot, isn't visible in either program, but Aviano Flare, right above it, is visible/usable in TextEdit but not visible/not usable in Entourage.
Now, to be clear, as far as I know all of my typefaces are currently showing up in Font Book, and about 95% of my fonts are visible in both Entourage and Text Edit, even though the 5% that's problematic is partially the same/ partially different in each. I hope I'm not going to have to open every single program I own to keep checking for variations—hopefully knowing that there *are* variations between programs will help someone to give me a suggestion.
If the 5% that don't work were the exact same, I was going to assume Mac voodoo. My lame workaround was going to be, to manually check my font folder against one program or the other, and copy every font that doesn't show up, back into the User folder. It would take quite a while, and there would be two copies, but at least the ones that are not visible to my programs would (hopefully?) be visible again.
But the ones that don't show up and therefore can't be used are not all the same. So this indicates worse voodoo, some sort of font management issue that I don't get, and it probably means I'd be at this check-and-copy thing forever with each and every program I use. Or, I could waste a lot of disk space, and copy all fonts to User. Ugh.
So I'm hoping that by laying out everything I *have* already tried this morning, someone will be able to spot a step I missed that will help me get Font Book to wrangle these darned typefaces better.
If Font Book *thinks* all fonts are now available to all users, how can I get my programs to agree—and get my programs also to "see" and let me use all of my fonts?
MacBook Pro, Mac OS X (10.7.5)
Font Book version 3

Answer 1

Okay!
So, should anyone else ever find themselves with this weird problem, here's what the rest of my day looked like—and yes, I did at last get the problems solved.
First I printed out a list of all my fonts (in the /Library/Fonts folder). Very long. Then I skimmed through the two programs standing in, hopefully, for every program, to try and see if something the problem fonts have in common would jump out at me.
One thing did: all of the "problem" fonts in TextEdit (the ones that didn't show up, in other words) were from a period when one of the type companies I use was automatically installing to a subfolder within the font folder (named with their company's name). Though TextEdit "sees" all the fonts in the Microsoft subfolder, apparently it can't handle other subfolders. So I removed all of these fonts from the company subfolder to the main /Fonts folder, and solved one problem. This problem, oddly, must have been there all along, but who uses a ton of fonts in TextEdit? So I didn't notice the problem until I was troubleshooting today, and thinking that was a nice neutral program to test things in.
But it did nothing for the problem in Entourage, which is where I began my day—even though *some* of Entourage's problem fonts were also in that subfolder, most were not, and the ones that were in that subfolder were still not made visible to Entourage by moving them out of it. So then I scrubbed the long, long list of fonts, looking for all the ones that were not visible in Entourage. Blech. That took a while.
When I got my complete list of missing fonts, I went back to Font Book and validated all of those fonts. I discovered that all but one, share one tiny problem: the "'name' table structure" error. (The final font did have a minor error in validation, but not that error.)
Now I didn't make a list early this morning, so I can't be sure that every one of these fonts was among the ones that started my attempt to clean up and make things right, but I'm assuming they are. I suppose it's possible that during the things I tried to fix the mess today, that one or two fonts actually started working on their own, but probably this list would be the same as one I could have made in the morning, back when I was young and innocent and thought I wouldn't need lists because it was all going to work with ease.
Before I got too excited, I then stopped and validated all the fonts I have. I wanted to make sure that this wasn't an error tons of fonts of mine have, in which case I had not located the problem. But in fact, only the typefaces I couldn't see in Entourage had this error. So I went back to the www to search for what to do about this error.
And in case anyone else needs to replicate my success, this is the site with the fix that worked for me on it:
http://www.iwebss.com/tech/540-fixing-fonts-with-validation-errors-on-mac
Skip down to where it says "Quick Instructions." Download the program suggested there, and do *exactly* what it says under Quick Instructions and no more (and please, make a folder with copies of any otfs or ttfs you need to do this with before you try the fix, in case it doesn't work for you as it did for me and you need to back up to the old versions).
One note: in those instructions, he doesn't mention that after "Save As," the program may hang up and give you a nasty message about access—just go to the Finder and do a Force Quit, no need to report, open the program again, and carry on. You haven't harmed the font or the program, and it does save before hanging up, so you can just go on to the next font in your list. For some miraculous reason, doing this does repair the "'name' table structure" error (and the error that the one odd font had as well!), and when I reopened Font Book, Entourage, and just for good measure, TextEdit, all of the fonts which had been plaguing me were perfectly visible and absolutely functional.
Thank you, Kurt, for your good ideas here and elsewhere on these forums. You were of great help to me today even before your answered this question.   Though I was so deep in troubleshooting that I didn't get back to see your latest reply, I appreciate your taking the time to try to guess at this very odd hiccup.
Why this error bothers some programs and not others... why it's so easy to fix, with a simple program that you purposely use to make absolutely no changes... who knows. But check your subfolders first, and if that's not the problem, try validating fonts and see if the "'name' table structure" error is at the root of your problems. Perhaps this will work for others.