Hello, thanks people.
I have had an email from the agent that the fare class booked was T, so I have sent this to Aegean. I do not mind if I only get 70% as with the Turkish segments. If I get 0, then Turkish has charged me for a Class T flight but sold me something cheaper. This seems like a fraud to me. Perhaps the agent did it through negligence i.e. my original print out clearly states Class T. I have never booked a 3 leg journey by any means which gave me different Fare Classes for any of the legs. Normally I book online and have no problems - I like the Austrian website which clearly states the Fare Class early on. Whereas the Lufthansa site hides this information until late in the payment process.
By the way I told the agent clearly I wanted to get all the miles and showed her the Aegean earning chart for Turkish before finalising the ticket. (I am already A3 Gold).
I found on Thai's ROP site that Lufthansa discount tickets do not earn any ROP miles on Thai segments - but they make no such statement for Austrian. ROP gives some miles for Thai Class G so I have joined that club to credit my Thai Class G international flights. I will also reuse my Miles and More membership in future, eg where Austrian Class T credits 50% on M@M vs 0% on A3. I have an Austrian Class T ticket for September which includes SYD-BKK so if I credit 100% to Aegean for SYD-BKK I may have the same problem all over again. M+M also gives 100% for Class T on Thai. I will ring M+M up before the trip.
If all else fails I can try to credit this March 2013 Thai flight to M+M with original boarding pass posted to Germany. Yet Aegean claims to have no access to my Eticket so how would Lufthansa do it?