Per ForsakenArcher, the next Lua update will "fix" an unintended display issue with the Turbine.UI.Window class. This class is supposed to be not visible by default, and will do so after this update goes live.
All authors should compensate for this change by specifically setting all windows to be visible, that should be visible by default eg:
Code:
myWindow:SetVisible(true);
No additional details were given, and no specific date was set for when this update will reach live.