Not totally the same issue, but I had a similar problem last year with Delta moving me and my wife out of our preferred main cabin seats (2-across) to C+ seats that were less desirable, and in spite of repeated attempts to put us back in original seats the Delta agent couldn't make it stick. (There was a thread about this at the time as others were having the same problem). The best the agents could figure out was that because I took the automatic C+ upgrade on our initial flight, on the return flight their software stuck us back in C+ even though we hadn't checked the box for an upgrade.

So maybe this had something to do with an upgrade on one leg of your trip, with some glitchy software algorithm dutifully moving you what they think is a "preferred" seat?