If you look at the A3 earning miles page you can see that your PE "O fare" should be earning 100% miles (which you knew) unless possibly if you booked your ticket before June 30, 2013 when I guess an O fare did not earn miles (but I don't know if you could have even bought an AC PE fare back then).

http://en.aegeanair.com/milesandbonu...on/earn-miles/

Maybe try calling A3 again and explaining that you bought a Premium ecomony ticket O fare with AC - that it was not a discounted economy ticket that you bought. It does appear that prior to June 30, 2013, A3 was not crediting any miles for an AC O fare