This is an issue with ver. 11 - when values are plotted inside segments, the automatic scale settings that you define in the Number tab, are not being used, and the whole number is presented instead.
Based on a recent blog by Rob Wunderlich, this problem is fixed in ver. 12. So, if you wait a little bit and upgrade to ver. 12, the problem will go away.
Until then, the only thing you can think of is a work around - for example, manually divide the number by 1000 and format the Axis accordingly.