You need to adjust manually the size and position of each window. Here is an example for the "Overhead" popup window int he panel.cfg file. Try this:

[Window05]
file_1024=OH.bmp
Background_color=16,16,16
size_mm=1200,1200
window_size_ratio=1.000 
position=0
visible=0
ident=12104
render_3d_window=0
window_size= 1.000, 1.000  // this is the width and height
window_pos= 0.000, 0.000 // this is the X and Y coordinates
zorder=10

[...]

Hope this helps...