Fonts not available in applications although installed

That's a large part of the problem. You have more than one font manager on your Mac. If you're not using Font Book, delete it. Then you need to reset its orphaned database so OS X stops trying to control which fonts are, or aren't active according to that data.

To remove Font Book from the hard drive, follow these steps:

1) Open Font Book, and then its preferences. Uncheck the box for "Alert me if system fonts change". Close the preferences and shut down Font Book. Put the Font Book application in the trash and delete it.

2) Restart your Mac and immediately hold down the Shift key when you hear the startup chime to boot into Safe Mode. Keep holding it until OS X asks you to log in (you will get this screen on a Safe Mode boot even if your Mac is set to automatically log in). Let the Mac finish booting to the desktop and then restart normally.

This will reset Font Book's database and clear the cache files in your user account. The main goal in this step is to remove the orphaned Font Book database from the hard drive. With the Font Book application no longer on the hard drive, a new one cannot be created. Which is what we want.

3) Close all running applications. From an administrator account, open the Terminal app and enter the following command. You can also copy/paste it from here into the Terminal window:

sudo atsutil databases -remove

This removes all font cache files. Both for the system and all user font cache files. After running the command, close Terminal and immediately restart your Mac.

Okay, try this one next. The previous stuff only resets the cache files of your account.

Close all running applications. From an administrator account, open the Terminal app and enter the following command. You can also copy/paste it from here into the Terminal window:

sudo atsutil databases -remove

Terminal will then ask for you to enter your admin password. As you type, it will not show anything, so be sure to enter it correctly.

This removes all font cache files. Both for the system and the current user font cache files. After running the command, close Terminal and immediately restart your Mac.

Now this may not change anything, but will certainly eliminate cache files as the problem one way or the other.

Hmm. So the fonts are active through Font Book, but not Suitcase or FEX. Can't say I've ever seen that one before. If fonts work in one (especially the finicky Font Book), then they normally work with any other font manager.

A bit of a long shot - also the blunt approach. Have you tried reinstalling the OS? Or the shorter route that often fixes many issues; reapplying the 10.6.8 Combo updater?

Yup, that's the one. 🙂 I suggested it because I have helped people with problems similar to yours (and myself) where fonts just plain wouldn't work on an up-to-date system. But reinstall the OS, and everything works again.

I reinstalled my OS but basically nothing changed.

Oh well, as least you know you've got a nice clean install at the moment. If you haven't yet, I'd go through the steps again to remove Font Book.

So basically for some reason the fonts interfere with each other.
However this wasn't always the case...

So I really don't get it why suddenly they can't be shown together...

They are conflicting. All fonts have internal names. Those are the ones that actually mean something to the OS, and are the ones that appear in your font lists. The file names on the desktop mean nothing. They're for your reference only so you know what font that file is.

Read my article, Font Management in OS X, chapters 12 and 13. It explains what a font conflict is and why you're seeing the problems you are with those fonts.

Sorry to have put you the long way around on this. I took your initial comment, "I have installed with Font Explorer X, what won't show up in ANY application.", as fonts that just plain wouldn't work, not a conflict with other fonts.

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Every name must be unique. A really obvious problem is the menu name. Literally, the name that appears in your application menus. Both are Block Berthold. So only one or the other can appear in your lists. The OS or your apps will never show the exact same name twice. Not only is it still a conflict, if it were allowed, you would have no idea which one you were choosing until you started typing.

Whoops! I goofed. The menu name is the same from font to font in a family. The one I don't believe is correct is the PS Font Name of VlackBE-ExtraCnIt. Which is the same for both fonts. Change it on each font to be the same as the FOND name. Do not click the Build Style Name, or Build Names buttons. Click Apply and generate the fonts again and see if they work as expected.

Weird. I guess I'd have to see them, but am much too busy right now.