In rare cases, MathType may fail to convert OMML (Equation Builder) objects to MathType objects using its Convert Equations functionality.
If you encounter this problem, try saving your file to DOC format and then resaving the file as a DOCX file. This forces Word to "rehydrate" the OMML objects and may flush out the corruption that was preventing MathType from converting them.
Once you have successfully run the MathType Conversion function, remember to proof the new MathType objects carefully against the original OMML equations. For example, not all of the characters in the font used by the Equation Builder will necessarily be accurately mapped to the font used by MathType.
If you use this workaround, remember not to open your DOC version of the file in Word 2003 or an earlier version of Word before resaving as DOCX - if you open the DOC file in a version of Word that does not support OMML objects, the internal code necessary to reconstruct them will be permanently lost.