Gah, the problem was quite simple actually. The code now works all the time and hordes are always active (with decent AI scripts - try the one in VM 0.93 for instance for that)

<hordes>
<end_target_faction_bonus int="500"/>
<start_target_faction_bonus int="400"/>
<farming_level_bonus int="50"/>
<shared_target_bonus int="0"/>
<disbanding_horde_bonus int="-300"/>
<starting_region_bonus int="910"/>
<horde_target_resource_bonus int="990"/>
</hordes>

basically moved 10 from shared_target_bonus to starting_region_bonus