So, I think I have fixed the missing fonts in InDesign problem. (This was also an issues in other CS5 programs but I mostly work in InDesign.)

If you use a font manager tool, it may include a feature which “reactivates fonts at startup”. In the case of FontAgent Pro, it gives you two options in its prefs: reactivate manually activated fonts and auto-activated fonts. These are checked on as a default.

By unchecking the “reactivates fonts at startup” options, fonts are loading up lickity split with no missing fonts.

Note: this is not auto-activation (these are the program specific plug ins). Actually, by deactivating the auto startup option, the auto-activation works much faster.

I can't blame Insider as, they are just seeing this issue now and only for special cases, like mine and; it is also partly due to Apple and Adobe and how the whole complex font management system in the OS works and changes all the time. But since all the font managers are neck and neck with features, if you run into a similar issue, you might deactivate any start up font auto-activation feature.

BTW: over the years I have owned versions of Master Juggler, Suitcase, ATM, Font Reserve (which was great in OS9). They are all good solutions. I still like FontAgent Pro because I can call them and speak to a human. That is more important than anything else.