The same issue was frustrating me for a long time. I'm unsure if this problem is easier to handle in newer versions of ArcMap, but certainly in 10.3 I was surprised to find this was the resolution.
Converting labels to annotation in a geodatabase locks in a single reference scale. This is no good if you have Data Driven Pages with differing scales.
By converting labels to annotation In the map, you are then able to go into the Data Frame properties > Annotation Groups tab and you will see a new Group has been created. Turn off the <Default> Group and change the Reference Scale on the newly created Group to <None>.