I feel for you. I flew YEG-YUL on January 17th and then a few days later YYZ-YEG on Flex G fares both times and AC tried to only credit me 25% MP and 0 segment.
A call to the MP Gold desk, a discussion with an agent, a personalized e-mail to me acknowledging the issue and promising to take it up with AC saw my MP account properly credited with 100% and proper segment count earlier this week.