I've confirmed bag window height is currently hard-coded to assume 4 slot columns. This means bags with more than 4 columns will have extra space (empty rows) at th bottom. Those with less than 4 columns will have rows at the bottom clipped.
I've requested SOE port the Hotkey window sizing code and icon sizer window call to the bag window. Its now officially on their schedule for next LU (though they can't promis anything).
What this should do is give us in-game, individually configurable bags. Future Bags should allow right-click access to the icon sizer window to set the icon size individually for each bag. Each bag will also be resizable, with the same snap to nearest icon edge features of a Hotkey window. So any bag can be set to any number of columns, with any icon size
