Same situation for me, really irritating. I had 23.5k miles in first year (13k by TK flights) and get downgraded to classic. In every information they provided me at the begining of the challenge was no word that those 15k miles should be collected by TK flights.
I've created ticket in their customer support, but didn't get an answer for 6 days now. I'm writing messages to them on Twitter (@TK_HelpDesk account), but they only respond that my case is in progress.