ToME: the Tales of Maj'Eyal

I have few games with them being friendly and on some others they are hostile.
Any reason to that?

They are hostile to anyone with spells (runes are spells).

by runes you meen infusions?

Nope, runes. Both runes and infusions are inscriptions. Runes are magic based inscriptions, infusions are nature based inscriptions.

runes are red as item, infusions are green as item.

If you don't have any runes, look through your talents and see if any of them say "Is A Spell". Even if you're not a magic user by default, you can gain talents from rescuing escortees that count as spells, and therefore make Ziguranths angry.

also, racial talents.
and undead are also enemies to everyone, regardless of your skills, if you don't wear your cloak of deception. (which i think should be renamed to cloak of peace)