As it is entirely plausible that such a routing on Swiss could earn absolutelty nothing in Miles&Bonus, there is some crucial information missing here.
Were all flights actually operated by Swiss? What is the airline code that appears on each flight segment (is it LX, or are there others?). And which booking classes were you travelling in?
Almost half of all Swiss economy classes earn nothing in Aegean. Therefore it is important to know what booking classes your ticket was issued in. It is also very important to know if there were any codeshares in play.