I was ready to report similar cases for my routes as well, thinking this was a major bug. I was getting the 3200ish miles for the direct flight DUS-ATH and just the 3000ish miles for the 2-segment routing via SKG, which made 0 sense, since I used to get over 4000 miles for that routing.
However, I soon noticed that this was due to the fact that the 2-segment routing only offered all-economy for the domestic part, which booked into H! After I was actually able to find a routing via SKG, where both legs were indeed in business class, I did get the correct mileage displayed.
Then again, these Lisbon and Dublin issues are of a totally different nature, since the U, T, P fares for comfort flex seem to offer more miles than the mid-priced fares and almost as much as the full economy fare! I would think that these are temporary glitches or oversights and that they will be corrected in due time, but I wouldn't bet money that whoever books now won't have issues crediting the correct amount of miles!
Aegean's IT wins again...