This is a little odd but it seems that data coming from our SDE server won't show in browser windows that are maximized on large screens. I am fortunate enough to have a 30" monitor and when I maximize the flex viewer browser window I can still see the basemaps but not any operational layers. I have to reduce the window down in order for the mapping information to appear. It seems to be able to handle the height of 1600 just not the width of 2560. I have to reduce it below 2087 wide before data appears.
It's also interesting to note that I can see my own basemap layer (cached aerial) at any window size. So it's something to do with the operational layers only.
