This is likely an issue more with the folks at Mathtype than it is in Scrivener. I’ve emailed their text support and have yet to receive a response.
Essentially, when I type equations in Mathtype certain symbols appear as plain boxes. These boxes then carry themselves over to Scrivener when I copy and paste them. I’m wondering if anyone has figured out a workaround or knows how to resolve this. I don’t know if it’s Mathtype, Scrivener, or a system wide issue.