Thanks for the great feedback, MrMathType and Maria!
In the example tests I provided, you did notice I switched to Euclid Symbol for several exercises as I had a hunch that good, old Symbol font was causing problems. I've yet to see any issues with Euclid Symbol so far.
Just to confirm what we've been seeing in our tests so far: If only 1 character exists in an .eps using Symbol font, any or all other characters in the .eps (even those in different fonts) are also at risk of disappearing?
Any idea why characters would go missing (in the presence of Symbol font) more often with embedded Mathtype vs. Mathtype that is placed in InDesign?