Well, I just talked to Insider and got a solution but not one that I am really happy with. I am used to being able to open my computer and just work. But now in OS X, that won't work any more. I can't have my fonts auto activated on start up. Now what I have to do is every day, go in and activate the set of fonts for each of my projects to be able to work.
That sounds bogus to me, but I'm a Windows user.
I'd clear caches again, and delete any AdobeFnt*.lst files (* is a two-digit number).
Why can't you have your fonts auto-activate? The plug-ins for FontAgent Pro have all been updated, and should work as expected. I'm using FAPro as well, and don't have any problems with auto-activation. One thing you MAY be experiencing, however, is a "false" message from InDesign stating fonts are missing, since that dialogue frequently pops up before FAPro has had the chance to activate them (providing auto-activation is on); wait a few seconds, and the fonts should activate. Here is a screen shot of my Preferences for FAPro.
By checking "Show feedback", you'll notice when FAPro actually activates the font(s) in question. Note, however, that SOME fonts are not auto-activated for some reason, and I've found that some of these are older fonts, with similar names to currently activated ones. For instance, on our systems, if "Fournier MT-Regualr" is activated or auto-activated, the font "Fournier MT-RegularSC" will be ignored, even if it's used in the document; in which case, we have to open FAPro and manually activate it.
Additionally, you can check the "Include manually activated fonts" and "Include auto-activated fonts" in the preferences, and this will open them every time you startup/login. This feature is great for us.
Another thing to try, from InDesign, is once you get the "font missing..." message, try opening "Find Font" from the "Type" menu. I've noticed that simply invoking "Find Font" triggers a call to FAPro to auto-activate. It works with us many times, but again not every time.
Anyway, hope your issue is solved or at least answered--it can be frustrating.
Thanks. I'll look into this. Here's the odd thing. Now only Times and Helvetica are turned on... and yet now the fonts are showing up in the doc. Hmmmm......
Keep in mind that some fonts may also be in the Adobe Fonts folders, too, and they'd show up even if FAP isn't activating them elsewhere.
I was having a similar issue. I know this post is from years ago, but I was able to solve the issue so I am posting in hopes that someone else who is having this problem and stumbles across this post will find it helpful:
I noticed that some of the fonts I was using had there name showing up in green text in Windows Explorer, this means that they are encrypted files. I simply unencrypted the files, re-installed the fonts, and then restarted InDesign - Presto! All is right in the world. Hope this helped!