I have office 2016 and mathtype 6.9b. The formulas in the word seem correct but after conversion to pdf, they become upper relative to the main line as I have attached bellow.
First one is to save the file in previous word version format and after this convert it to pdf.
And the second one is to use special converter to make pdf, like doPdf, which uses the printer drivers for converting. But in such way you receive pdf file as a picture. Also there are many converters in internet.
Finally, I had the same problem in previous Office versions and I did this: I've open each formula in the document through mathtype to make the reload and after this the formulas are displayed correctly.
Though there might be many solutions to your problem, but I found this method ( https://www.youtube.com/watch?v=9YGTH4WrY_8) to be quite effective in terms of typing equations, numbering them, inserting any kind of symbols (similar to latex) and conversion to PDF as well, without any issues.