Okay so your not using the normal way to include a header or footer that everyone else does as in header and footer templates in vbulletin admin.
Well given the way there new hack system works I do not think there is anything I can tweak here for you real quick. We call their global.php file and prep the header and navbar and footer templates for display and any other associated java scripts etc.
So since we call global.php your new hack system is called and works fine but as you see you have issue with it printing header in big window display.
The issue is simple but there is no easy solution here. We print the header based on variables we set to call header navbar templates etc and define them $vbheader $vbfooter. If we set them to NO which we do on showfull they are not displayed however your plugin system is called in global.php
The quick solution would be to place your header and footer in the normal templates assigned for these in vb
admin but I am assuming you have a reason for not doing so.