As in my previous thread 'Long loading and saving times', I have had similar issues.
But you have had more luck, getting response from developers (pshaw).
I don't think it's to do with your machine specs, as mine meets the requirements.
I have disabled auto-save, and are playing on huge map in stead of gigantic, in the hope the problem does not resurface.
But worried that after playing many turns, the problem will come back.
The issue needs fixing.