This is a question posted on May 1st, 2015 and it was identified as bug for secured services. I suppose that it was resolved with the latest version of the web appbuilder.
However, when I use feature services that are not secure, the problem persists. After you open the AT for the first time, whatever changes you make (turn on or off) on the layers afterwards, the attribute table does not refresh. Even if I click on "refresh" or change the map extent.
Also, when you use a filter and the result is not within the current map extent, the AT shows no results. When you zoom out, then the AT shows the result. Can this be changed to show the results of queries regardless of the map extent?