MTKnife thanks for the bug reports and sorry you're having these issues. Please be post any additional details you can gather ... what Rep were you with Lumotte? Which missions from Calgan?
As for Lumotte, I think my Mok rep was -27 or so? I've noticed that the rep for these missions can be slightly negative (a -7 Zenrin rep didn't cause a problem with Guun a couple of nights ago)--however, the striking thing in the case(s) I mentioned was that Lumotte went through the "However..." dialog, where he says I'm "not in good standing with my people," but then gave me the story mission immediately anyway.
In Faen's case, it would have been the "Political Crusade" missions he offers after you complete "Arbiter Neutrality".