Ho risolto, ho modificaato i seguenti metodi:

public void internalFrameIconified(InternalFrameEvent e) {
if(e.getSource()==frame1){
frame2.setPreferredSize(new Dimension(900,280));
}else{
frame1.setPreferredSize(new Dimension(1015,250));
}
}

public void internalFrameDeiconified(InternalFrameEvent e) {
if(e.getSource()==frame1){
frame2.setPreferredSize(new Dimension(900,90));
}else{
frame1.setPreferredSize(new Dimension(1015,180));
}
}