in all GeoGebra versions, it is very annoying, to achieve exactly the applet dimensions you want. At the moment I see only one way, to get exactly, what I want: I change the window dimensions with the mouse pixel for pixel and look at the dimensions shown in the html export dialogue again and again, to get information about the dimensions, the applet will have after export. When I have found the wanted dimensions, I can export the applet. That worked better with older GeoGebra versions than with GeoGebra 4.2.0, because since we have those nice new tool bars at the top of the construction, we have to guess, how many pixels they add to the height of the graphics view. Ythis extra height will not be added at the top of the construction, but on the bottom.
I have no easy answer to this problems and don't know, if it is possible to make it easy to get applets with the wanted dimensions. It may be, that it would be easier, to get a preview of the applet dimensions, if it was possible, to hide all tool bars, especially those, that won't show in the applet. Another idea is to show the dimensions of the graphics view via a short key or so.