If you open a document that uses a font that's not installed, and the OS knows where it's at, it will offer to install it. It's a one shot thing, it won't ask for that font again if you allow the installation.
I don't think that's quite what's happening here. I think these messages result from opening a document that uses a font that's
installed but not
activated; the OS is offering to activate that font, and if you agree, the font stays activated until you quit the application.
In theory, you can control this behavior in Font Book's prefs (although Google reveals that it was problematic in early versions of 10.5): there's a checkbox for
Automatic font activation and, below that, one for
Ask me before activating. It sounds like kevs' system is behaving as if the second box is checked as well as the first. However, I get these font dialogs from time to time, and
Ask me before activating is
not checked in my Font Book prefs, so the whole automatic font activation thing may still be flakey.
The many discussions at Apple on this topic seem to have in common the label "This question is
not answered."