MathType and PowerMath use vastly different methods for nudging. PowerMath nudges have no equivalent in MathType, so MathMonarch must disregard PowerMath nudges when building into MathType.

For example, an 'a' with a tilde nudged over the top of it will look like this in PowerMath or MathType:
with the WWdoc equivalent of [&a*N*[6.0%3.5]|tilde|&]

When rebuilt into MathType, it will look like this:

Nudge problems such as this can be avoided by using the correct characters, and using nudges as little as possible. Any nudge conversion problems that you encounter will have to be handled on a manual basis.