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...

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...

http://www.adobe.com/devnet/pdf/pdf_reference.html