Converting Maplex labels to annotation sets WordSpacing to a value other than 100. If CharacterSpacing is set to something other than 0, that value in the annotation is also incorrect in the annotation feature class, which changes the Override values.
Perform a field calculation on the WordSpacing field (calculate to "100" without quotes) and on the CharacterSpacing field (calculate to "15" without quotes). This should have negligible effects on the display. However, once these two calculations are performed, the Override value will be reset to 0.