Could have a lot to do with the role she was playing. Early Liz was a meaty role. Liz had two huge secrets and was trying to normalize David and protect him from the Roger's indifference. She also had to contend with Burke on at least two fronts. She also had to deal with multiple problems (large and small) stemming from Mathew Morgan, Bill Malloy, Carolyn, and Roger. And this was all pretty much at the same time. I would guess that Joan played Liz as a woman with all these problems nuanced in her performance as opposed to playing Liz as a woman whose only problem was the one she was dealing with in any particular scene. I don't think her last characters had as much to deal with all at once and perhaps it came across as a phoned-in performance in comparison. Could have had as much to do with the writing also, I would guess (as I am not that familiar with the last storylines).
On the other hand, as you've stated, it has been noted that much of the cast had grown tired of "the job" toward the series' end and were ready to "move on". So I guess if Joan had been in that camp, it may have manifested itself in her performance.
