Try this Agathorn. Maybe it'll work maybe it wont. But take your include out of mainhud.xml and say put it in an random file that has mainhud_*.xml for example I'll use the group window.
<?xml version="1.0" encoding="utf-8"?>
<include>you_file_here</include>
<Page ... the normal window code here >
...
</Page>
This basically does the same thing as putting it in mainhud.xml but its added via the eq2ui_mainhud.group.xml file. Maybe it'll trick it into saveing its spot.