I’ve just encountered this problem, or at least observed the same behaviour, where the email address remains as it was after altering it and clicking save in the System Console.
In my case a user had registered with an invalid email address (TLD was missing). In the end I manually altered the email address directly in the database, after which they were able to log in.
I suspect the fact that the address was invalid somehow prevented me from changing it via the System Console… Hopefully this helps to track down what appears to be a bug.
Possibly related (?): Cannot change email address with patch user API