Thanks, that makes sense. I ended up packing a pbo, now works perfectly.

I made a faction by merely changing the side of an existing one from blufor to opfor and exporting the full faction cfg to description.ext. Then I changed the faction name in the description.ext. This is the method mentioned here :

Editing an existing addon: select the faction and change the side/flag but leave the name and classname the same. If you make no changes to the units loadouts you can simply apply the faction config at the mission level by pasting it into description.ext. This is a quick and easy way to change the side or name of a faction for a one off mission whilst leaving everything else intact.

The correct groups spawn in the military module but they keep their original side (blufor in the map) and start shooting each other.

Also in the wiki it mentions the possibility of creating a group by mixing units from different factions and using the same method (description.ext) but it seems that the only way of doing that is to create new units which is not possible with this method, is there any alternative?