SAM's e-mail notices in fact mean you have strike teams idling. It's a bug introduced with patch 1.05. No reason to check for e-mails before you finish a priority or allies mission.
Loyalty mission progress depends on different missions you completed (not tasks, these do not affect it). If it's currently ON HOLD, do some other mission, it'll unlock eventually. That goes both for Peebee's remnant scanner and Cora's whichever step.
Finally, if you didn't receive any e-mail and a mission is not on hold in journal anymore, go talk to your crewmember.
Talking to peebee does nothing. No email diddly squat. Why is this game so ridden with bugs when bethesda make massive games that are much less simple with less problems, or at least they fix the issues. SORT IT OUT EA!!!
