I'm using Windows, so my advice may be worth nothing...
1) You shouldn't have to deactivate to get ID to recognize fonts.
2) Design Science gives its fonts away in Type 1 and Truetype flavors. If one doesn't work (the Type 1 version has given me trouble) maybe the other one will.
3) Indesign should be able to recognize fonts installed through the OS; that is, the "install fonts manual for Indesign" (I didn't know there was one) should be saying, basically, install your fonts the same way for Indesign that you do for every other program.
4) Are you really *copying* from Illustrator to Indesign, or are you copying from Mathtype to Illustrator and then saving an AI file and Placing that?
I worry about copying between the programs, so perhaps do an experiment where you compare pasting with placing. But first off, I'd skip the step of putting fonts in the Indesign folder, apparently it hasn't worked. Search your entire system and delete all but one copy of MT Extra. Make sure you've only got one version of Symbol too, if possible. If you download the free Font Explorer from Linotype, you can get it to consolidate all of your fonts which makes it easy to spot and delete extra copies. It could be that Indesign and Mathtype are using slightly different versions of fonts with the same names. Note that Adobe, MathType, and Apple have all kindly provided you with a font called Symbol, and while they're mostly the same, they aren't quite, and if different programs prefer different Symbol fonts you may get the empty character boxes. I found Font Explorer invaluable to get rid of duplicate Symbol fonts.
Create an equation that uses an MT Extra character, also throw in some large brackets (like parentheses around a fraction) and some other stuff that you typically use. Save it as an eps file.
Distill the eps file to pdf.
Copy the equation material to the clipboard.
Now go to Indesign and try three methods of placing it in the file: paste it. Place the eps. Place the pdf. View as high quality, and try printing the page. If one of these methods works better than the other, I'd use it from now on. And do your best not to change your Symbol font once you've got one that works. I once made that mistake and could no longer print older MathType equations until I reopened and saved them. And I had a lot at the time...
Hi RodneyA: I tried your ideas. First I see what you mean about
having a font problem. You pointed me in the right direction.
I got onboard "Font Explorer" (I still need to learn how to more
fully use this) but anyway, then I was able to identify which
MathType fonts where giving me trouble. I did this by selecting a
single character from MathType and pasting it into illustrator. Now
illustrator opens the glyph pallet for that font, so that I can see
what font the character belongs to. Then in FontExplorer I find that
font and deactivated it. Next, I see that MathType no longer has
that font available; O.K. then I go back to FontExplorer and
reactivate the font, but now FontExplore gives me options (activate
this one and deactivate all the other copies of this font that occur
in other folders. I say yes, and Activate the font. Then I open an
Indesign file that had trouble with that font (the boxes) and guess
what -- they are FIXED! Yeah I discovered in this way that both
MT Extra and Euclid Math 2 had the problem and I fixed in the above
manner. You saved me! Thanks . Its all working now.
Ooh, I must have deleted too much stuff out of my reply email. Here's what I meant to say:
Excellent. It's nice having a piece of software monitoring your font collections. I'd recommend taking the working Symbol and MT Extra fonts and making a font collection that you can turn off and on when you work on this projects, so that you'll get the right one. Or, if you're sure (and you've backed up recently), delete the ones that don't work.
But do keep your eyes open for the weirdnesses that I've noticed -- they're usually either the tall fences (parens or brackets around a fraction, for instance) and some "special" math characters (for instance, Greek alphabet is fine, but the upside-down Delta or the curly d for derivative) disappear on printing. If that happens, try distilling the MathType eps file.
I'm trying to do some preventative reading and found the section on Text and Annex D somewhat useful (link via Adobe Digital Editions, sort of) though I'll see when my project gets closer to print. These forums have been helpful...