Seat map is the same as it was when we booked and chose the seats, and agent also said no equipment change was made.
I've never had a problem calling and requesting the companion(s) be seated in MCE with me. I can think of at least 6 trips in the past 2 years where this was done without any issue. In this case, even as a non-elite, she was moved from 9B to 8F - which is another MCE seat, so that doesn't make sense either considering there are still a fair number of non-MCE seats available.
That is a different question than whether there was an entitlement to the seat assignment. Agents can always assign seats and waive the fees. The question is whether the assignment sticks. Entirely possible that a software upgrade does a more aggressive sweep or that you just got unlucky.