On the subject of alliances, could it be that some of the factions are getting stuck in alliance webs? Faction A was going to attack B but allies with C who are allied with B causing a ceasefire? I'm not sure if the AI even remotely respects these things when deciding what to do, but I find if the alliance is with another AI faction they are much less likely to break it.
Edit - this obviously wouldn't explain not attacking the Eleutheroi towns in most cases, but the Casse start neutral with the Eleutheroi, I think.
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