Do you remember what branded fare you were on (e.g. Standard / Flex / Comfort / Latitude)? On a recent trip, ATL-YYZ last month, I was on a V "Standard" fare, 014- (AC) ticket, which was credited to TK with only 50% miles instead of the 100% (according to the TK chart). The same V "Standard" earned 0 (e.g. it did not credit) on the domestic YYZ-YOW segment.

This makes me believe that it's the branded fare, in addition to the fare class, that will dictate how it is credited to TK. This is apparently also the experience with those in the A3 M+B program (there is a separate thread on AC fares in the A3 forum).

So far, this has only been an issue with economy class tickets (not PE or J).