We have recently been receiving reports about FX Equations equations not lining up in Word 2016. Initially we thought that we were causing the issue but Microsoft has just announced that the issue lies with a particular version of Word 2016 (16.0.4498.1000).
The full discussion can be read here:
This discussion is referring specifically to MathType and Equation Editor but our products utilise the same features and are being similarly affected.
At this point in time there does not seem to be a resolution available to the issue but it seems that Microsoft is definitely aware of the problem and working on a solution.