To the OP and others that had this happen and you didn't get back into MCE, has American ever given you any compensation?
I know they are not obligated to do anything, but especially for EXP and CK, it's a pretty terrible experience. I can't find a logical explanation for it that would make it ok.
As a follow up, have you been able to use EF AC chance alert to proactively change your seats when it happens?